From 2c75e6005445c3170e07bbc2fa8a9dbf54f7d3ad Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 20 Feb 2024 15:30:09 +0000 Subject: [PATCH 01/28] Template update for nf-core/tools version 2.13 --- .editorconfig | 9 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/branch.yml | 2 +- .github/workflows/ci.yml | 7 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 17 +- .github/workflows/linting.yml | 12 +- .github/workflows/linting_comment.yml | 4 +- .github/workflows/release-announcements.yml | 11 +- README.md | 5 +- assets/multiqc_config.yml | 2 + assets/schema_input.json | 21 +- bin/check_samplesheet.py | 259 ----------- conf/modules.config | 8 - lib/NfcoreTemplate.groovy | 356 -------------- lib/Utils.groovy | 47 -- lib/WorkflowMain.groovy | 77 --- lib/WorkflowRnafusion.groovy | 122 ----- main.nf | 100 ++-- modules.json | 28 +- modules/local/samplesheet_check.nf | 31 -- .../dumpsoftwareversions/environment.yml | 7 - .../custom/dumpsoftwareversions/main.nf | 24 - .../custom/dumpsoftwareversions/meta.yml | 37 -- .../templates/dumpsoftwareversions.py | 102 ---- .../dumpsoftwareversions/tests/main.nf.test | 43 -- .../tests/main.nf.test.snap | 33 -- .../dumpsoftwareversions/tests/tags.yml | 2 - modules/nf-core/fastqc/tests/main.nf.test | 14 +- .../nf-core/fastqc/tests/main.nf.test.snap | 76 ++- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/tests/main.nf.test | 13 +- .../nf-core/multiqc/tests/main.nf.test.snap | 32 +- nextflow.config | 5 +- nextflow_schema.json | 1 + pyproject.toml | 8 +- subworkflows/local/input_check.nf | 44 -- .../utils_nfcore_rnafusion_pipeline/main.nf | 247 ++++++++++ .../nf-core/utils_nextflow_pipeline/main.nf | 126 +++++ .../nf-core/utils_nextflow_pipeline/meta.yml | 38 ++ .../tests/main.function.nf.test | 54 +++ .../tests/main.function.nf.test.snap | 12 + .../tests/main.workflow.nf.test | 123 +++++ .../tests/nextflow.config | 9 + .../utils_nextflow_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfcore_pipeline/main.nf | 440 ++++++++++++++++++ .../nf-core/utils_nfcore_pipeline/meta.yml | 24 + .../tests/main.function.nf.test | 134 ++++++ .../tests/main.function.nf.test.snap | 138 ++++++ .../tests/main.workflow.nf.test | 29 ++ .../tests/main.workflow.nf.test.snap | 15 + .../tests/nextflow.config | 9 + .../utils_nfcore_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfvalidation_plugin/main.nf | 62 +++ .../utils_nfvalidation_plugin/meta.yml | 44 ++ .../tests/main.nf.test | 200 ++++++++ .../tests/nextflow_schema.json | 96 ++++ .../utils_nfvalidation_plugin/tests/tags.yml | 2 + workflows/rnafusion.nf | 133 ++---- 61 files changed, 2108 insertions(+), 1406 deletions(-) delete mode 100755 bin/check_samplesheet.py delete mode 100755 lib/NfcoreTemplate.groovy delete mode 100644 lib/Utils.groovy delete mode 100755 lib/WorkflowMain.groovy delete mode 100755 lib/WorkflowRnafusion.groovy delete mode 100644 modules/local/samplesheet_check.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml delete mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml delete mode 100644 subworkflows/local/input_check.nf create mode 100644 subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 9b990088..dd9ffa53 100644 --- a/.editorconfig +++ b/.editorconfig @@ -18,7 +18,12 @@ end_of_line = unset insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset -indent_size = unset +[/subworkflows/nf-core/**] +charset = unset +end_of_line = unset +insert_final_newline = unset +trim_trailing_whitespace = unset +indent_style = unset [/assets/email*] indent_size = unset @@ -28,5 +33,5 @@ indent_size = unset indent_style = unset # ignore python -[*.{py}] +[*.{py,md}] indent_style = unset diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index a4b6b4d3..b46a4819 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index cf29b8fd..104df35b 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 476d72a8..19704d23 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@v2 + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 31823f13..bdbc1fcb 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,13 +28,16 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 with: version: "${{ matrix.NXF_VER }}" + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index e37cfda5..0b6b1f27 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@v9 + - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 8611458a..f823210d 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download' # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: + inputs: + testbranch: + description: "The specific branch you wish to utilize for the test execution of nf-core download." + required: true + default: "dev" pull_request: types: - opened @@ -23,13 +28,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" - - uses: eWaterCycle/setup-singularity@v7 + - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: singularity-version: 3.8.3 @@ -42,13 +47,13 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./ run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ @@ -64,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 81cd098e..748b4311 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Set up Python 3.11 - uses: actions/setup-python@v5 + uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: 3.11 cache: "pip" @@ -32,12 +32,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 147bcd10..b706875f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@v3 + uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@v2 + uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 21ac3f06..c3674af2 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -9,6 +9,11 @@ jobs: toot: runs-on: ubuntu-latest steps: + - name: get topics and convert to hashtags + id: get_topics + run: | + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -20,11 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} + ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics + send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +63,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@v0.1.0 + - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/README.md b/README.md index c48b6f3b..ca941ca5 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,9 @@ nf-core/rnafusion -[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnafusion/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnafusion/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) + +[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index b8874305..c070b89c 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -11,3 +11,5 @@ report_section_order: order: -1002 export_plots: true + +disable_version_detection: true diff --git a/assets/schema_input.json b/assets/schema_input.json index aff11de1..fa630b6c 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,25 +10,22 @@ "sample": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" + "errorMessage": "Sample name must be provided and cannot contain spaces", + "meta": ["id"] }, "fastq_1": { "type": "string", + "format": "file-path", + "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", - "anyOf": [ - { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$" - }, - { - "type": "string", - "maxLength": 0 - } - ] + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, "required": ["sample", "fastq_1"] diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index 4a758fe0..00000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,259 +0,0 @@ -#!/usr/bin/env python - - -"""Provide a command line tool to validate and transform tabular samplesheets.""" - - -import argparse -import csv -import logging -import sys -from collections import Counter -from pathlib import Path - -logger = logging.getLogger() - - -class RowChecker: - """ - Define a service that can validate and transform each given row. - - Attributes: - modified (list): A list of dicts, where each dict corresponds to a previously - validated and transformed row. The order of rows is maintained. - - """ - - VALID_FORMATS = ( - ".fq.gz", - ".fastq.gz", - ) - - def __init__( - self, - sample_col="sample", - first_col="fastq_1", - second_col="fastq_2", - single_col="single_end", - **kwargs, - ): - """ - Initialize the row checker with the expected column names. - - Args: - sample_col (str): The name of the column that contains the sample name - (default "sample"). - first_col (str): The name of the column that contains the first (or only) - FASTQ file path (default "fastq_1"). - second_col (str): The name of the column that contains the second (if any) - FASTQ file path (default "fastq_2"). - single_col (str): The name of the new column that will be inserted and - records whether the sample contains single- or paired-end sequencing - reads (default "single_end"). - - """ - super().__init__(**kwargs) - self._sample_col = sample_col - self._first_col = first_col - self._second_col = second_col - self._single_col = single_col - self._seen = set() - self.modified = [] - - def validate_and_transform(self, row): - """ - Perform all validations on the given row and insert the read pairing status. - - Args: - row (dict): A mapping from column headers (keys) to elements of that row - (values). - - """ - self._validate_sample(row) - self._validate_first(row) - self._validate_second(row) - self._validate_pair(row) - self._seen.add((row[self._sample_col], row[self._first_col])) - self.modified.append(row) - - def _validate_sample(self, row): - """Assert that the sample name exists and convert spaces to underscores.""" - if len(row[self._sample_col]) <= 0: - raise AssertionError("Sample input is required.") - # Sanitize samples slightly. - row[self._sample_col] = row[self._sample_col].replace(" ", "_") - - def _validate_first(self, row): - """Assert that the first FASTQ entry is non-empty and has the right format.""" - if len(row[self._first_col]) <= 0: - raise AssertionError("At least the first FASTQ file is required.") - self._validate_fastq_format(row[self._first_col]) - - def _validate_second(self, row): - """Assert that the second FASTQ entry has the right format if it exists.""" - if len(row[self._second_col]) > 0: - self._validate_fastq_format(row[self._second_col]) - - def _validate_pair(self, row): - """Assert that read pairs have the same file extension. Report pair status.""" - if row[self._first_col] and row[self._second_col]: - row[self._single_col] = False - first_col_suffix = Path(row[self._first_col]).suffixes[-2:] - second_col_suffix = Path(row[self._second_col]).suffixes[-2:] - if first_col_suffix != second_col_suffix: - raise AssertionError("FASTQ pairs must have the same file extensions.") - else: - row[self._single_col] = True - - def _validate_fastq_format(self, filename): - """Assert that a given filename has one of the expected FASTQ extensions.""" - if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): - raise AssertionError( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) - - def validate_unique_samples(self): - """ - Assert that the combination of sample name and FASTQ filename is unique. - - In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the - number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. - - """ - if len(self._seen) != len(self.modified): - raise AssertionError("The pair of sample name and FASTQ must be unique.") - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - row[self._sample_col] = f"{sample}_T{seen[sample]}" - - -def read_head(handle, num_lines=10): - """Read the specified number of lines from the current position in the file.""" - lines = [] - for idx, line in enumerate(handle): - if idx == num_lines: - break - lines.append(line) - return "".join(lines) - - -def sniff_format(handle): - """ - Detect the tabular format. - - Args: - handle (text file): A handle to a `text file`_ object. The read position is - expected to be at the beginning (index 0). - - Returns: - csv.Dialect: The detected tabular format. - - .. _text file: - https://docs.python.org/3/glossary.html#term-text-file - - """ - peek = read_head(handle) - handle.seek(0) - sniffer = csv.Sniffer() - dialect = sniffer.sniff(peek) - return dialect - - -def check_samplesheet(file_in, file_out): - """ - Check that the tabular samplesheet has the structure expected by nf-core pipelines. - - Validate the general shape of the table, expected columns, and each row. Also add - an additional column which records whether one or two FASTQ reads were found. - - Args: - file_in (pathlib.Path): The given tabular samplesheet. The format can be either - CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. - file_out (pathlib.Path): Where the validated and transformed samplesheet should - be created; always in CSV format. - - Example: - This function checks that the samplesheet follows the following structure, - see also the `viral recon samplesheet`_:: - - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - - .. _viral recon samplesheet: - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv - - """ - required_columns = {"sample", "fastq_1", "fastq_2"} - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_in.open(newline="") as in_handle: - reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) - # Validate the existence of the expected header columns. - if not required_columns.issubset(reader.fieldnames): - req_cols = ", ".join(required_columns) - logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") - sys.exit(1) - # Validate each row. - checker = RowChecker() - for i, row in enumerate(reader): - try: - checker.validate_and_transform(row) - except AssertionError as error: - logger.critical(f"{str(error)} On line {i + 2}.") - sys.exit(1) - checker.validate_unique_samples() - header = list(reader.fieldnames) - header.insert(1, "single_end") - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_out.open(mode="w", newline="") as out_handle: - writer = csv.DictWriter(out_handle, header, delimiter=",") - writer.writeheader() - for row in checker.modified: - writer.writerow(row) - - -def parse_args(argv=None): - """Define and immediately parse command line arguments.""" - parser = argparse.ArgumentParser( - description="Validate and transform a tabular samplesheet.", - epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", - ) - parser.add_argument( - "file_in", - metavar="FILE_IN", - type=Path, - help="Tabular input samplesheet in CSV or TSV format.", - ) - parser.add_argument( - "file_out", - metavar="FILE_OUT", - type=Path, - help="Transformed output samplesheet in CSV format.", - ) - parser.add_argument( - "-l", - "--log-level", - help="The desired log level (default WARNING).", - choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), - default="WARNING", - ) - return parser.parse_args(argv) - - -def main(argv=None): - """Coordinate argument parsing and program execution.""" - args = parse_args(argv) - logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") - if not args.file_in.is_file(): - logger.error(f"The given input file {args.file_in} was not found!") - sys.exit(2) - args.file_out.parent.mkdir(parents=True, exist_ok=True) - check_samplesheet(args.file_in, args.file_out) - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/conf/modules.config b/conf/modules.config index d91c6aba..e3ea8fa6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,14 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: SAMPLESHEET_CHECK { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: FASTQC { ext.args = '--quiet' } diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy deleted file mode 100755 index e248e4c3..00000000 --- a/lib/NfcoreTemplate.groovy +++ /dev/null @@ -1,356 +0,0 @@ -// -// This file holds several functions used within the nf-core pipeline template. -// - -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - -class NfcoreTemplate { - - // - // Check AWS Batch related parameters have been specified correctly - // - public static void awsBatch(workflow, params) { - if (workflow.profile.contains('awsbatch')) { - // Check params.awsqueue and params.awsregion have been set if running on AWSBatch - assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - } - } - - // - // Warn if a -profile or Nextflow config has not been provided to run the pipeline - // - public static void checkConfigProvided(workflow, log) { - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - } - - // - // Generate version string - // - public static String version(workflow) { - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string - } - - // - // Construct and send completion email - // - public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { - - // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" - } - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = NfcoreTemplate.version(workflow) - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" - } - } - - // Check if we are only sending emails on failure - def email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$projectDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$projectDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] - def sf = new File("$projectDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - Map colors = logColours(params.monochrome_logs) - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") - sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] - } - mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" - } - } - - // Write summary e-mail HTML to a file - def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); - output_hf.delete() - - // Write summary e-mail TXT to a file - def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); - output_tf.delete() - } - - // - // Construct and send a notification to a web server as JSON - // e.g. Microsoft Teams and Slack - // - public static void IM_notification(workflow, params, summary_params, projectDir, log) { - def hook_url = params.hook_url - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = NfcoreTemplate.version(workflow) - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("$projectDir/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); - } - } - - // - // Dump pipeline parameters in a json file - // - public static void dump_parameters(workflow, params) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) - - FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") - temp_pf.delete() - } - - // - // Print pipeline summary on completion - // - public static void summary(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" - } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } - } - - // - // ANSII Colours used for terminal logging - // - public static Map logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes - } - - // - // Does what is says on the tin - // - public static String dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" - } - - // - // nf-core logo - // - public static String logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String workflow_version = NfcoreTemplate.version(workflow) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) - } -} diff --git a/lib/Utils.groovy b/lib/Utils.groovy deleted file mode 100644 index 8d030f4e..00000000 --- a/lib/Utils.groovy +++ /dev/null @@ -1,47 +0,0 @@ -// -// This file holds several Groovy functions that could be useful for any Nextflow pipeline -// - -import org.yaml.snakeyaml.Yaml - -class Utils { - - // - // When running with -profile conda, warn if channels have not been set-up appropriately - // - public static void checkCondaChannels(log) { - Yaml parser = new Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } - - if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy deleted file mode 100755 index b8a1723f..00000000 --- a/lib/WorkflowMain.groovy +++ /dev/null @@ -1,77 +0,0 @@ -// -// This file holds several functions specific to the main.nf workflow in the nf-core/rnafusion pipeline -// - -import nextflow.Nextflow - -class WorkflowMain { - - // - // Citation string for pipeline - // - public static String citation(workflow) { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - // TODO nf-core: Add Zenodo DOI for pipeline after first release - //"* The pipeline\n" + - //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" - } - - - // - // Validate parameters and print summary to screen - // - public static void initialise(workflow, params, log, args) { - - // Print workflow version and exit on --version - if (params.version) { - String workflow_version = NfcoreTemplate.version(workflow) - log.info "${workflow.manifest.name} ${workflow_version}" - System.exit(0) - } - - // Check that a -profile or Nextflow config has been provided to run the pipeline - NfcoreTemplate.checkConfigProvided(workflow, log) - // Check that the profile doesn't contain spaces and doesn't end with a trailing comma - checkProfile(workflow.profile, args, log) - - // Check that conda channels are set-up correctly - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - Utils.checkCondaChannels(log) - } - - // Check AWS batch settings - NfcoreTemplate.awsBatch(workflow, params) - - // Check input has been provided - if (!params.input) { - Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - } - } - // - // Get attribute from genome config file e.g. fasta - // - public static Object getGenomeAttribute(params, attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null - } - - // - // Exit pipeline if --profile contains spaces - // - private static void checkProfile(profile, args, log) { - if (profile.endsWith(',')) { - Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - if (args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - } -} diff --git a/lib/WorkflowRnafusion.groovy b/lib/WorkflowRnafusion.groovy deleted file mode 100755 index 1e289fdc..00000000 --- a/lib/WorkflowRnafusion.groovy +++ /dev/null @@ -1,122 +0,0 @@ -// -// This file holds several functions specific to the workflow/rnafusion.nf in the nf-core/rnafusion pipeline -// - -import nextflow.Nextflow -import groovy.text.SimpleTemplateEngine - -class WorkflowRnafusion { - - // - // Check and validate parameters - // - public static void initialise(params, log) { - - genomeExistsError(params, log) - - - if (!params.fasta) { - Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - } - } - - // - // Get workflow summary for MultiQC - // - public static String paramsSummaryMultiqc(workflow, summary) { - String summary_section = '' - for (group in summary.keySet()) { - def group_params = summary.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

$group

\n" - summary_section += "
\n" - for (param in group_params.keySet()) { - summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" - } - summary_section += "
\n" - } - } - - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" - return yaml_file_text - } - - // - // Generate methods description for MultiQC - // - - public static String toolCitationText(params) { - - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def citation_text = [ - "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text - } - - public static String toolBibliographyText(params) { - - // TODO Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " - ].join(' ').trim() - - return reference_text - } - - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = run_workflow.toMap() - meta["manifest_map"] = run_workflow.manifest.toMap() - - // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - //meta["tool_bibliography"] = toolBibliographyText(params) - - - def methods_text = mqc_methods_yaml.text - - def engine = new SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html - } - - // - // Exit pipeline if incorrect --genome key provided - // - private static void genomeExistsError(params, log) { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - } - } -} diff --git a/main.nf b/main.nf index 47c38e5e..91475247 100644 --- a/main.nf +++ b/main.nf @@ -13,66 +13,96 @@ nextflow.enable.dsl = 2 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` -params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') +include { RNAFUSION } from './workflows/rnafusion' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnafusion_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_rnafusion_pipeline' + +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_rnafusion_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE & PRINT PARAMETER SUMMARY + GENOME PARAMETER VALUES ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { validateParameters; paramsHelp } from 'plugin/nf-validation' - -// Print help message if needed -if (params.help) { - def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) - def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - -WorkflowMain.initialise(workflow, params, log, args) +// TODO nf-core: Remove this line if you don't need a FASTA file +// This is an example of how to use getGenomeAttribute() to fetch parameters +// from igenomes.config using `--genome` +params.fasta = getGenomeAttribute('fasta') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOW FOR PIPELINE + NAMED WORKFLOWS FOR PIPELINE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { RNAFUSION } from './workflows/rnafusion' - // -// WORKFLOW: Run main nf-core/rnafusion analysis pipeline +// WORKFLOW: Run main analysis pipeline depending on type of input // workflow NFCORE_RNAFUSION { - RNAFUSION () -} + take: + samplesheet // channel: samplesheet read in from --input + + main: + + // + // WORKFLOW: Run pipeline + // + RNAFUSION ( + samplesheet + ) + + emit: + multiqc_report = RNAFUSION.out.multiqc_report // channel: /path/to/multiqc_report.html + +} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN ALL WORKFLOWS + RUN MAIN WORKFLOW ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// -// WORKFLOW: Execute a single named workflow for the pipeline -// See: https://github.com/nf-core/rnaseq/issues/619 -// workflow { - NFCORE_RNAFUSION () + + main: + + // + // SUBWORKFLOW: Run initialisation tasks + // + PIPELINE_INITIALISATION ( + params.version, + params.help, + params.validate_params, + params.monochrome_logs, + args, + params.outdir, + params.input + ) + + // + // WORKFLOW: Run main workflow + // + NFCORE_RNAFUSION ( + PIPELINE_INITIALISATION.out.samplesheet + ) + + // + // SUBWORKFLOW: Run completion tasks + // + PIPELINE_COMPLETION ( + params.email, + params.email_on_fail, + params.plaintext_email, + params.outdir, + params.monochrome_logs, + params.hook_url, + NFCORE_RNAFUSION.out.multiqc_report + ) } /* diff --git a/modules.json b/modules.json index a7097920..6d161c68 100644 --- a/modules.json +++ b/modules.json @@ -5,22 +5,36 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] - }, "fastqc": { "branch": "master", - "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", + "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", + "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", "installed_by": ["modules"] } } + }, + "subworkflows": { + "nf-core": { + "utils_nextflow_pipeline": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + }, + "utils_nfcore_pipeline": { + "branch": "master", + "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "installed_by": ["subworkflows"] + }, + "utils_nfvalidation_plugin": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + } + } } } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 9226705d..00000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,31 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/rnafusion/bin/ - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml deleted file mode 100644 index 9b3272bc..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: custom_dumpsoftwareversions -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf deleted file mode 100644 index f2187611..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_single' - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - template 'dumpsoftwareversions.py' -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml deleted file mode 100644 index 5f15a5fd..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,37 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - dump - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" -maintainers: - - "@drpatelh" - - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100755 index e55b8d43..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python - - -"""Provide functions to merge multiple versions.yml files.""" - - -import platform -from textwrap import dedent - -import yaml - - -def _make_versions_html(versions): - """Generate a tabular HTML output of all versions for MultiQC.""" - html = [ - dedent( - """\\ - - - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") - return "\\n".join(html) - - -def main(): - """Load all version files and generate merged output.""" - versions_this_module = {} - versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, - } - - with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - - # aggregate versions by the module name (derived from fully-qualified process name) - versions_by_module = {} - for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), - } - - with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) - with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) - - -if __name__ == "__main__": - main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test deleted file mode 100644 index b1e1630b..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ /dev/null @@ -1,43 +0,0 @@ -nextflow_process { - - name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "../main.nf" - process "CUSTOM_DUMPSOFTWAREVERSIONS" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "dumpsoftwareversions" - tag "custom/dumpsoftwareversions" - - test("Should run without failures") { - when { - process { - """ - def tool1_version = ''' - TOOL1: - tool1: 0.11.9 - '''.stripIndent() - - def tool2_version = ''' - TOOL2: - tool2: 1.9 - '''.stripIndent() - - input[0] = Channel.of(tool1_version, tool2_version).collectFile() - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.mqc_yml[0]).readLines()[0..10], - file(process.out.yml[0]).readLines()[0..7] - ).match() - } - ) - } - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap deleted file mode 100644 index 5f59a936..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "Should run without failures": { - "content": [ - [ - "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" - ], - [ - "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", - " \\n\\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n \\n \\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n\\n\\n \\n\\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.11.7", - " yaml: 5.4.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-09T23:01:18.710682" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24a..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 1f21c664..70edae4d 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_single") } ) } } @@ -63,7 +63,7 @@ nextflow_process { { assert path(process.out.html[0][1][0]).text.contains("") }, { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } @@ -89,7 +89,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } ) } } @@ -115,7 +115,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } ) } } @@ -153,7 +153,7 @@ nextflow_process { { assert path(process.out.html[0][1][2]).text.contains("") }, { assert path(process.out.html[0][1][3]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } ) } } @@ -179,7 +179,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } ) } } @@ -204,7 +204,7 @@ nextflow_process { { assert process.success }, { assert snapshot(process.out.html.collect { file(it[1]).getName() } + process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match() } + process.out.versions ).match("fastqc_stub") } ) } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 5d624bb8..86f7c311 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,5 +1,17 @@ { - "sarscov2 single-end [fastq] - stub": { + "fastqc_versions_interleaved": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:07.293713" + }, + "fastqc_stub": { "content": [ [ "test.html", @@ -7,14 +19,70 @@ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:40:57.254299" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:31:01.425198" + }, + "fastqc_versions_multiple": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:55.797907" + }, + "fastqc_versions_bam": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:26.795862" + }, + "fastqc_versions_single": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:27.043675" + }, + "fastqc_versions_paired": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:47.584191" }, - "versions": { + "fastqc_versions_custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:36:50.033627" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 7625b752..2212096a 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.19 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1b9f7c43..354f4430 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index d0438eda..f1c4242e 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + tag "modules" tag "modules_nfcore" tag "multiqc" @@ -12,7 +13,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -25,7 +26,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_single") } ) } @@ -36,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] @@ -49,7 +50,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_config") } ) } } @@ -61,7 +62,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -75,7 +76,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match() } + process.out.versions ).match("multiqc_stub") } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index d37e7304..c204b488 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,21 +1,41 @@ { - "versions": { + "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:02:49.911994" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:28:51.744211298" }, - "sarscov2 single-end [fastqc] - stub": { + "multiqc_stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:03:14.524346" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:28.847433492" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:13.223621555" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index b52cb3ab..fc563542 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,9 +16,7 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - - - // MultiQC options + fasta = null// MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null @@ -43,7 +41,6 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options // Defaults only, expecting to be overwritten diff --git a/nextflow_schema.json b/nextflow_schema.json index 3acf2be1..025bd65d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,6 +16,7 @@ "type": "string", "format": "file-path", "exists": true, + "schema": "assets/schema_input.json", "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", "description": "Path to comma-separated file containing information about the samples in the experiment.", diff --git a/pyproject.toml b/pyproject.toml index 7d08e1c8..56110621 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,11 +3,13 @@ [tool.ruff] line-length = 120 target-version = "py38" -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] cache-dir = "~/.cache/ruff" -[tool.ruff.isort] +[tool.ruff.lint] +select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] + +[tool.ruff.lint.isort] known-first-party = ["nf_core"] -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index 0aecf87f..00000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,44 +0,0 @@ -// -// Check input samplesheet and get read channels -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet // file: /path/to/samplesheet.csv - - main: - SAMPLESHEET_CHECK ( samplesheet ) - .csv - .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channel(it) } - .set { reads } - - emit: - reads // channel: [ val(meta), [ reads ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channel(LinkedHashMap row) { - // create meta map - def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() - - // add path(s) of the fastq file(s) to the meta map - def fastq_meta = [] - if (!file(row.fastq_1).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" - } - if (meta.single_end) { - fastq_meta = [ meta, [ file(row.fastq_1) ] ] - } else { - if (!file(row.fastq_2).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" - } - fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] - } - return fastq_meta -} diff --git a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf new file mode 100644 index 00000000..dc90ad90 --- /dev/null +++ b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf @@ -0,0 +1,247 @@ +// +// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { fromSamplesheet } from 'plugin/nf-validation' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' +include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' + +/* +======================================================================================== + SUBWORKFLOW TO INITIALISE PIPELINE +======================================================================================== +*/ + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + help // boolean: Display help text + validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + input // string: Path to input samplesheet + + main: + + ch_versions = Channel.empty() + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + pre_help_text = nfCoreLogo(monochrome_logs) + post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + UTILS_NFVALIDATION_PLUGIN ( + help, + workflow_command, + pre_help_text, + post_help_text, + validate_params, + "nextflow_schema.json" + ) + + // + // Check config provided to the pipeline + // + UTILS_NFCORE_PIPELINE ( + nextflow_cli_args + ) + // + // Custom validation for pipeline parameters + // + validateInputParameters() + + // + // Create channel from input file provided through params.input + // + Channel + .fromSamplesheet("input") + .map { + meta, fastq_1, fastq_2 -> + if (!fastq_2) { + return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { + validateInputSamplesheet(it) + } + .map { + meta, fastqs -> + return [ meta, fastqs.flatten() ] + } + .set { ch_samplesheet } + + emit: + samplesheet = ch_samplesheet + versions = ch_versions +} + +/* +======================================================================================== + SUBWORKFLOW FOR PIPELINE COMPLETION +======================================================================================== +*/ + +workflow PIPELINE_COMPLETION { + + take: + email // string: email address + email_on_fail // string: email address sent on pipeline failure + plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published + monochrome_logs // boolean: Disable ANSI colour codes in log output + hook_url // string: hook URL for notifications + multiqc_report // string: Path to MultiQC report + + main: + + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + + // + // Completion email and summary + // + workflow.onComplete { + if (email || email_on_fail) { + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + } + + completionSummary(monochrome_logs) + + if (hook_url) { + imNotification(summary_params, hook_url) + } + } +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ +// +// Check and validate pipeline parameters +// +def validateInputParameters() { + genomeExistsError() +}// +// Validate channels from input samplesheet +// +def validateInputSamplesheet(input) { + def (metas, fastqs) = input[1..2] + + // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + if (!endedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + } + + return [ metas[0], fastqs ] +} +// +// Get attribute from genome config file e.g. fasta +// +def getGenomeAttribute(attribute) { + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + return params.genomes[ params.genome ][ attribute ] + } + } + return null +} + +// +// Exit pipeline if incorrect --genome key provided +// +def genomeExistsError() { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } +}// +// Generate methods description for MultiQC +// +def toolCitationText() { + // TODO nf-core: Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text +} + +def toolBibliographyText() { + // TODO nf-core: Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text +} + +def methodsDescriptionText(mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = workflow.toMap() + meta["manifest_map"] = workflow.manifest.toMap() + + // Pipeline DOI + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + // meta["tool_bibliography"] = toolBibliographyText() + + + def methods_text = mqc_methods_yaml.text + + def engine = new groovy.text.SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html.toString() +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf new file mode 100644 index 00000000..ac31f28f --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -0,0 +1,126 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NEXTFLOW_PIPELINE { + + take: + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results + check_conda_channels // boolean: check conda channels + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && outdir) { + dumpParametersToJSON(outdir) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } + + emit: + dummy_emit = true +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(outdir) { + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = JsonOutput.toJson(params) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + Yaml parser = new Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } + + if (channels_missing | channel_priority_violation) { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml new file mode 100644 index 00000000..e5c3a0a8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -0,0 +1,38 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NEXTFLOW_PIPELINE" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" + - "@drpatelh" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..8ed4310c --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -0,0 +1,54 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assertAll( + { assert function.success } + ) + } + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..db2030f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,12 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "v9.9.9" + ], + "timestamp": "2024-01-19T11:32:36.031083" + }, + "Test Function checkCondaChannels": { + "content": null, + "timestamp": "2024-01-19T11:32:50.456" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..f7c54bc6 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,123 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NEXTFLOW_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + workflow "UTILS_NEXTFLOW_PIPELINE" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Should run no inputs") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = false + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should print version") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = true + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } + ) + } + } + + test("Should dump params") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = params.outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should not create params JSON if no output directory") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = null + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config new file mode 100644 index 00000000..53574ffe --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml new file mode 100644 index 00000000..f8476112 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nextflow_pipeline: + - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf new file mode 100644 index 00000000..a8b55d6f --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -0,0 +1,440 @@ +// +// Subworkflow with utility functions specific to the nf-core pipeline template +// + +import org.yaml.snakeyaml.Yaml +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFCORE_PIPELINE { + + take: + nextflow_cli_args + + main: + valid_config = checkConfigProvided() + checkProfileProvided(nextflow_cli_args) + + emit: + valid_config +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Warn if a -profile or Nextflow config has not been provided to run the pipeline +// +def checkConfigProvided() { + valid_config = true + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + valid_config = false + } + return valid_config +} + +// +// Exit pipeline if --profile contains spaces +// +def checkProfileProvided(nextflow_cli_args) { + if (workflow.profile.endsWith(',')) { + error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } + if (nextflow_cli_args[0]) { + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } +} + +// +// Citation string for pipeline +// +def workflowCitation() { + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + " ${workflow.manifest.doi}\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" +} + +// +// Generate workflow version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + Yaml yaml = new Yaml() + versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + $workflow.manifest.name: ${getWorkflowVersion()} + Nextflow: $workflow.nextflow.version + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions + .unique() + .map { processVersionsFromYAML(it) } + .unique() + .mix(Channel.of(workflowVersionToYAML())) +} + +// +// Get workflow summary for MultiQC +// +def paramsSummaryMultiqc(summary_params) { + def summary_section = '' + for (group in summary_params.keySet()) { + def group_params = summary_params.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    $group

    \n" + summary_section += "
    \n" + for (param in group_params.keySet()) { + summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + + return yaml_file_text +} + +// +// nf-core logo +// +def nfCoreLogo(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} + +// +// Return dashed line +// +def dashedLine(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + +// +// ANSII colours used for terminal logging +// +def logColours(monochrome_logs=true) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// +// Attach the multiqc report to email +// +def attachMultiqcReport(multiqc_report) { + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + if (multiqc_report) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + } + return mqc_report +} + +// +// Construct and send completion email +// +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + + // Set up the e-mail variables + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + if (!workflow.success) { + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + } + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = getWorkflowVersion() + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = attachMultiqcReport(multiqc_report) + + // Check if we are only sending emails on failure + def email_address = email + if (!email && email_on_fail && !workflow.success) { + email_address = email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("${workflow.projectDir}/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("${workflow.projectDir}/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + Map colors = logColours(monochrome_logs) + if (email_address) { + try { + if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { + // Catch failures and try with plaintext + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + mail_cmd.execute() << email_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + } + } + + // Write summary e-mail HTML to a file + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() +} + +// +// Print pipeline summary on completion +// +def completionSummary(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params, hook_url) { + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = getWorkflowVersion() + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml new file mode 100644 index 00000000..d08d2434 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -0,0 +1,24 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PIPELINE" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - nextflow_cli_args: + type: list + description: | + Nextflow CLI positional arguments +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..1dc317f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -0,0 +1,134 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function checkProfileProvided") { + + function "checkProfileProvided" + + when { + function { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function workflowCitation") { + + function "workflowCitation" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function nfCoreLogo") { + + function "nfCoreLogo" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dashedLine") { + + function "dashedLine" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function without logColours") { + + function "logColours" + + when { + function { + """ + input[0] = true + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function with logColours") { + function "logColours" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..10f948e6 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,138 @@ +{ + "Test Function checkProfileProvided": { + "content": null, + "timestamp": "2024-02-09T15:43:55.145717" + }, + "Test Function checkConfigProvided": { + "content": [ + true + ], + "timestamp": "2024-01-19T11:34:13.548431224" + }, + "Test Function nfCoreLogo": { + "content": [ + "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" + ], + "timestamp": "2024-01-19T11:34:38.840454873" + }, + "Test Function workflowCitation": { + "content": [ + "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" + ], + "timestamp": "2024-01-19T11:34:22.24352016" + }, + "Test Function without logColours": { + "content": [ + { + "reset": "", + "bold": "", + "dim": "", + "underlined": "", + "blink": "", + "reverse": "", + "hidden": "", + "black": "", + "red": "", + "green": "", + "yellow": "", + "blue": "", + "purple": "", + "cyan": "", + "white": "", + "bblack": "", + "bred": "", + "bgreen": "", + "byellow": "", + "bblue": "", + "bpurple": "", + "bcyan": "", + "bwhite": "", + "ublack": "", + "ured": "", + "ugreen": "", + "uyellow": "", + "ublue": "", + "upurple": "", + "ucyan": "", + "uwhite": "", + "iblack": "", + "ired": "", + "igreen": "", + "iyellow": "", + "iblue": "", + "ipurple": "", + "icyan": "", + "iwhite": "", + "biblack": "", + "bired": "", + "bigreen": "", + "biyellow": "", + "biblue": "", + "bipurple": "", + "bicyan": "", + "biwhite": "" + } + ], + "timestamp": "2024-01-19T11:35:04.418416984" + }, + "Test Function dashedLine": { + "content": [ + "-\u001b[2m----------------------------------------------------\u001b[0m-" + ], + "timestamp": "2024-01-19T11:34:55.420000755" + }, + "Test Function with logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "timestamp": "2024-01-19T11:35:13.436366565" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..8940d32d --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap new file mode 100644 index 00000000..d07ce54c --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -0,0 +1,15 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "timestamp": "2024-01-19T11:35:22.538940073" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config new file mode 100644 index 00000000..d0a926bf --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml new file mode 100644 index 00000000..ac8523c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfcore_pipeline: + - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf new file mode 100644 index 00000000..2585b65d --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -0,0 +1,62 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp } from 'plugin/nf-validation' +include { paramsSummaryLog } from 'plugin/nf-validation' +include { validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFVALIDATION_PLUGIN { + + take: + print_help // boolean: print help + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // boolean: validate parameters + schema_filename // path: JSON schema file, null to use default value + + main: + + log.debug "Using schema file: ${schema_filename}" + + // Default values for strings + pre_help_text = pre_help_text ?: '' + post_help_text = post_help_text ?: '' + workflow_command = workflow_command ?: '' + + // + // Print help message if needed + // + if (print_help) { + log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters(parameters_schema: schema_filename) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml new file mode 100644 index 00000000..3d4a6b04 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml @@ -0,0 +1,44 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFVALIDATION_PLUGIN" +description: Use nf-validation to initiate and validate a pipeline +keywords: + - utility + - pipeline + - initialise + - validation +components: [] +input: + - print_help: + type: boolean + description: | + Print help message and exit + - workflow_command: + type: string + description: | + The command to run the workflow e.g. "nextflow run main.nf" + - pre_help_text: + type: string + description: | + Text to print before the help message + - post_help_text: + type: string + description: | + Text to print after the help message + - validate_params: + type: boolean + description: | + Validate the parameters and error if invalid. + - schema_filename: + type: string + description: | + The filename of the schema to validate against. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test new file mode 100644 index 00000000..517ee54e --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -0,0 +1,200 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFVALIDATION_PLUGIN" + script "../main.nf" + workflow "UTILS_NFVALIDATION_PLUGIN" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "plugin/nf-validation" + tag "'plugin/nf-validation'" + tag "utils_nfvalidation_plugin" + tag "subworkflows/utils_nfvalidation_plugin" + + test("Should run nothing") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should run help") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with command") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with extra text") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = "pre-help-text" + post_help_text = "post-help-text" + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('pre-help-text') } }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } }, + { assert workflow.stdout.any { it.contains('post-help-text') } } + ) + } + } + + test("Should validate params") { + + when { + + params { + monochrome_logs = true + test_data = '' + outdir = 1 + } + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = true + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json new file mode 100644 index 00000000..7626c1c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "definitions": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml new file mode 100644 index 00000000..60b1cfff --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfvalidation_plugin: + - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 027a8b38..62c2cf15 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -1,54 +1,15 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - PRINT PARAMS SUMMARY + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' -def summary_params = paramsSummaryMap(workflow) - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -WorkflowRnafusion.initialise(params, log) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() -ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT LOCAL MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules -// -include { INPUT_CHECK } from '../subworkflows/local/input_check' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT NF-CORE MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Installed directly from nf-core/modules -// -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnafusion_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -56,50 +17,45 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// Info required for completion email and summary -def multiqc_report = [] - workflow RNAFUSION { - ch_versions = Channel.empty() + take: + ch_samplesheet // channel: samplesheet read in from --input - // - // SUBWORKFLOW: Read in samplesheet, validate and stage input files - // - INPUT_CHECK ( - file(params.input) - ) - ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema + main: + + ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() // // MODULE: Run FastQC // FASTQC ( - INPUT_CHECK.out.reads + ch_samplesheet ) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + // + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + .set { ch_collated_versions } // // MODULE: MultiQC // - workflow_summary = WorkflowRnafusion.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowRnafusion.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) MULTIQC ( ch_multiqc_files.collect(), @@ -107,31 +63,10 @@ workflow RNAFUSION { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList() ) - multiqc_report = MULTIQC.out.report.toList() -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - COMPLETION EMAIL AND SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.dump_parameters(workflow, params) - NfcoreTemplate.summary(workflow, params, log) - if (params.hook_url) { - NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) - } -} -workflow.onError { - if (workflow.errorReport.contains("Process requirement exceeds available memory")) { - println("🛑 Default resources exceed availability 🛑 ") - println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") - } + emit: + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From 05ffaee8e4b8a363e6654d20695504e498830b6e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 29 Feb 2024 16:11:57 +0000 Subject: [PATCH 02/28] Template update for nf-core/tools version 2.13.1 --- .devcontainer/devcontainer.json | 10 +---- .github/CONTRIBUTING.md | 14 ++++--- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/ci.yml | 2 +- .github/workflows/download_pipeline.yml | 2 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .gitpod.yml | 6 +-- README.md | 3 +- modules.json | 8 ++-- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 12 +++--- .../utils_nfcore_rnafusion_pipeline/main.nf | 10 +++-- .../tests/main.function.nf.test | 2 +- .../tests/main.function.nf.test.snap | 12 +++++- .../tests/main.workflow.nf.test | 20 ++------- .../tests/nextflow.config | 2 +- .../tests/main.function.nf.test.snap | 42 +++++++++++++++---- .../tests/main.workflow.nf.test.snap | 6 ++- .../tests/main.nf.test | 2 +- 23 files changed, 99 insertions(+), 74 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..b290e090 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -10,15 +10,7 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", - "python.formatting.yapfPath": "/opt/conda/bin/yapf", - "python.linting.flake8Path": "/opt/conda/bin/flake8", - "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", - "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.defaultInterpreterPath": "/opt/conda/bin/python" }, // Add the IDs of extensions you want installed when the container is created. diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index a0b73d5c..8e5d1fef 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,9 +9,8 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -:::info -If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)). -::: +> [!NOTE] +> If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow @@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: + +```bash +nf-test test --profile debug,test,docker --verbose +``` When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. @@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`. Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. -The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. +The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. ### Naming schemes diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index ed1d027b..8b85a0aa 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnaf - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnafusion/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/rnafusion _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index b46a4819..a4b6b4d3 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 104df35b..cf29b8fd 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bdbc1fcb..3390bf1a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index f823210d..08622fd5 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 748b4311..073e1876 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c3674af2..d468aeaa 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.gitpod.yml b/.gitpod.yml index 363d5b1d..105a1821 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -10,13 +10,11 @@ tasks: vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code + - charliermarsh.ruff # Code linter Ruff diff --git a/README.md b/README.md index ca941ca5..805de70e 100644 --- a/README.md +++ b/README.md @@ -7,12 +7,13 @@ [![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnafusion) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnafusion) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnafusion-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnafusion)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) diff --git a/modules.json b/modules.json index 6d161c68..5002e346 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", + "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2212096a..ca39fb67 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.20 + - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 354f4430..47ac352f 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : + 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index c204b488..bfebd802 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:28:51.744211298" + "timestamp": "2024-02-29T08:48:55.657331" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:28.847433492" + "timestamp": "2024-02-29T08:49:49.071937" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:13.223621555" + "timestamp": "2024-02-29T08:49:25.457567" } } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf index dc90ad90..c24a3741 100644 --- a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// Subworkflow with functionality specific to the nf-core/rnafusion pipeline // /* @@ -152,7 +152,9 @@ workflow PIPELINE_COMPLETION { // def validateInputParameters() { genomeExistsError() -}// +} + +// // Validate channels from input samplesheet // def validateInputSamplesheet(input) { @@ -190,7 +192,9 @@ def genomeExistsError() { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" error(error_string) } -}// +} + +// // Generate methods description for MultiQC // def toolCitationText() { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test index 8ed4310c..68718e4f 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -51,4 +51,4 @@ nextflow_function { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f8..e3f0baf4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index f7c54bc6..ca964ce8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -11,9 +11,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -39,9 +36,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -68,19 +62,16 @@ nextflow_workflow { test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -96,19 +87,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index 53574ffe..d0a926bf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -6,4 +6,4 @@ manifest { nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 10f948e6..1037232c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -1,25 +1,41 @@ { "Test Function checkProfileProvided": { "content": null, - "timestamp": "2024-02-09T15:43:55.145717" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" }, "Test Function checkConfigProvided": { "content": [ true ], - "timestamp": "2024-01-19T11:34:13.548431224" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" }, "Test Function nfCoreLogo": { "content": [ "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" ], - "timestamp": "2024-01-19T11:34:38.840454873" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:10.562934" }, "Test Function workflowCitation": { "content": [ "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" ], - "timestamp": "2024-01-19T11:34:22.24352016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" }, "Test Function without logColours": { "content": [ @@ -73,13 +89,21 @@ "biwhite": "" } ], - "timestamp": "2024-01-19T11:35:04.418416984" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" }, "Test Function dashedLine": { "content": [ "-\u001b[2m----------------------------------------------------\u001b[0m-" ], - "timestamp": "2024-01-19T11:34:55.420000755" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" }, "Test Function with logColours": { "content": [ @@ -133,6 +157,10 @@ "biwhite": "\u001b[1;97m" } ], - "timestamp": "2024-01-19T11:35:13.436366565" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap index d07ce54c..859d1030 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -10,6 +10,10 @@ ] } ], - "timestamp": "2024-01-19T11:35:22.538940073" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 517ee54e..5784a33f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -197,4 +197,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +} From 840c0f21c6f5ad570e1e37c58d974a96be1867ea Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 13:10:16 +0100 Subject: [PATCH 03/28] pre-commit for template merge 2.13.1 --- lib/NfcoreTemplate.groovy | 356 -------------- lib/Utils.groovy | 47 -- lib/WorkflowMain.groovy | 76 --- lib/WorkflowRnafusion.groovy | 122 ----- modules.json | 19 + .../utils_nfcore_rnafusion_pipeline/main.nf | 286 ++++++++++++ .../nf-core/utils_nextflow_pipeline/main.nf | 126 +++++ .../nf-core/utils_nextflow_pipeline/meta.yml | 38 ++ .../tests/main.function.nf.test | 54 +++ .../tests/main.function.nf.test.snap | 20 + .../tests/main.workflow.nf.test | 111 +++++ .../tests/nextflow.config | 9 + .../utils_nextflow_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfcore_pipeline/main.nf | 440 ++++++++++++++++++ .../nf-core/utils_nfcore_pipeline/meta.yml | 24 + .../tests/main.function.nf.test | 134 ++++++ .../tests/main.function.nf.test.snap | 166 +++++++ .../tests/main.workflow.nf.test | 29 ++ .../tests/main.workflow.nf.test.snap | 19 + .../tests/nextflow.config | 9 + .../utils_nfcore_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfvalidation_plugin/main.nf | 62 +++ .../utils_nfvalidation_plugin/meta.yml | 44 ++ .../tests/main.nf.test | 200 ++++++++ .../tests/nextflow_schema.json | 96 ++++ .../utils_nfvalidation_plugin/tests/tags.yml | 2 + workflows/rnafusion.nf | 57 ++- 27 files changed, 1926 insertions(+), 624 deletions(-) delete mode 100755 lib/NfcoreTemplate.groovy delete mode 100644 lib/Utils.groovy delete mode 100755 lib/WorkflowMain.groovy delete mode 100755 lib/WorkflowRnafusion.groovy create mode 100644 subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy deleted file mode 100755 index e248e4c3..00000000 --- a/lib/NfcoreTemplate.groovy +++ /dev/null @@ -1,356 +0,0 @@ -// -// This file holds several functions used within the nf-core pipeline template. -// - -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - -class NfcoreTemplate { - - // - // Check AWS Batch related parameters have been specified correctly - // - public static void awsBatch(workflow, params) { - if (workflow.profile.contains('awsbatch')) { - // Check params.awsqueue and params.awsregion have been set if running on AWSBatch - assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - } - } - - // - // Warn if a -profile or Nextflow config has not been provided to run the pipeline - // - public static void checkConfigProvided(workflow, log) { - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - } - - // - // Generate version string - // - public static String version(workflow) { - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string - } - - // - // Construct and send completion email - // - public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { - - // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" - } - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = NfcoreTemplate.version(workflow) - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" - } - } - - // Check if we are only sending emails on failure - def email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$projectDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$projectDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] - def sf = new File("$projectDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - Map colors = logColours(params.monochrome_logs) - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") - sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] - } - mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" - } - } - - // Write summary e-mail HTML to a file - def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); - output_hf.delete() - - // Write summary e-mail TXT to a file - def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); - output_tf.delete() - } - - // - // Construct and send a notification to a web server as JSON - // e.g. Microsoft Teams and Slack - // - public static void IM_notification(workflow, params, summary_params, projectDir, log) { - def hook_url = params.hook_url - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = NfcoreTemplate.version(workflow) - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("$projectDir/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); - } - } - - // - // Dump pipeline parameters in a json file - // - public static void dump_parameters(workflow, params) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) - - FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") - temp_pf.delete() - } - - // - // Print pipeline summary on completion - // - public static void summary(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" - } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } - } - - // - // ANSII Colours used for terminal logging - // - public static Map logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes - } - - // - // Does what is says on the tin - // - public static String dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" - } - - // - // nf-core logo - // - public static String logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String workflow_version = NfcoreTemplate.version(workflow) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) - } -} diff --git a/lib/Utils.groovy b/lib/Utils.groovy deleted file mode 100644 index 8d030f4e..00000000 --- a/lib/Utils.groovy +++ /dev/null @@ -1,47 +0,0 @@ -// -// This file holds several Groovy functions that could be useful for any Nextflow pipeline -// - -import org.yaml.snakeyaml.Yaml - -class Utils { - - // - // When running with -profile conda, warn if channels have not been set-up appropriately - // - public static void checkCondaChannels(log) { - Yaml parser = new Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } - - if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy deleted file mode 100755 index 550682a3..00000000 --- a/lib/WorkflowMain.groovy +++ /dev/null @@ -1,76 +0,0 @@ -// -// This file holds several functions specific to the main.nf workflow in the nf-core/rnafusion pipeline -// - -import nextflow.Nextflow - -class WorkflowMain { - - // - // Citation string for pipeline - // - public static String citation(workflow) { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - " https://doi.org/10.5281/zenodo.151721952\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" - } - - - // - // Validate parameters and print summary to screen - // - public static void initialise(workflow, params, log, args) { - - // Print workflow version and exit on --version - if (params.version) { - String workflow_version = NfcoreTemplate.version(workflow) - log.info "${workflow.manifest.name} ${workflow_version}" - System.exit(0) - } - - // Check that a -profile or Nextflow config has been provided to run the pipeline - NfcoreTemplate.checkConfigProvided(workflow, log) - // Check that the profile doesn't contain spaces and doesn't end with a trailing comma - checkProfile(workflow.profile, args, log) - - // Check that conda channels are set-up correctly - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - Utils.checkCondaChannels(log) - } - - // Check AWS batch settings - NfcoreTemplate.awsBatch(workflow, params) - - // Check input has been provided - if (!params.input) { - Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - } - } - // - // Get attribute from genome config file e.g. fasta - // - public static Object getGenomeAttribute(params, attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null - } - - // - // Exit pipeline if --profile contains spaces - // - private static void checkProfile(profile, args, log) { - if (profile.endsWith(',')) { - Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - if (args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - } -} diff --git a/lib/WorkflowRnafusion.groovy b/lib/WorkflowRnafusion.groovy deleted file mode 100755 index 1e289fdc..00000000 --- a/lib/WorkflowRnafusion.groovy +++ /dev/null @@ -1,122 +0,0 @@ -// -// This file holds several functions specific to the workflow/rnafusion.nf in the nf-core/rnafusion pipeline -// - -import nextflow.Nextflow -import groovy.text.SimpleTemplateEngine - -class WorkflowRnafusion { - - // - // Check and validate parameters - // - public static void initialise(params, log) { - - genomeExistsError(params, log) - - - if (!params.fasta) { - Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - } - } - - // - // Get workflow summary for MultiQC - // - public static String paramsSummaryMultiqc(workflow, summary) { - String summary_section = '' - for (group in summary.keySet()) { - def group_params = summary.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" - } - summary_section += "
    \n" - } - } - - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" - return yaml_file_text - } - - // - // Generate methods description for MultiQC - // - - public static String toolCitationText(params) { - - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def citation_text = [ - "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text - } - - public static String toolBibliographyText(params) { - - // TODO Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " - ].join(' ').trim() - - return reference_text - } - - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = run_workflow.toMap() - meta["manifest_map"] = run_workflow.manifest.toMap() - - // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - //meta["tool_bibliography"] = toolBibliographyText(params) - - - def methods_text = mqc_methods_yaml.text - - def engine = new SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html - } - - // - // Exit pipeline if incorrect --genome key provided - // - private static void genomeExistsError(params, log) { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - } - } -} diff --git a/modules.json b/modules.json index d5c7ee3d..a926bbcb 100644 --- a/modules.json +++ b/modules.json @@ -111,6 +111,25 @@ "installed_by": ["modules"] } } + }, + "subworkflows": { + "nf-core": { + "utils_nextflow_pipeline": { + "branch": "master", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "installed_by": ["subworkflows"] + }, + "utils_nfcore_pipeline": { + "branch": "master", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "installed_by": ["subworkflows"] + }, + "utils_nfvalidation_plugin": { + "branch": "master", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "installed_by": ["subworkflows"] + } + } } } } diff --git a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf new file mode 100644 index 00000000..dec3e3d8 --- /dev/null +++ b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf @@ -0,0 +1,286 @@ +// +// Subworkflow with functionality specific to the nf-core/rnafusion pipeline +// + +import groovy.json.JsonSlurper + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' +include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' + +/* +======================================================================================== + SUBWORKFLOW TO INITIALISE PIPELINE +======================================================================================== +*/ + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + help // boolean: Display help text + validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + + main: + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + pre_help_text = nfCoreLogo(monochrome_logs) + post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --genome_base } --outdir " + UTILS_NFVALIDATION_PLUGIN ( + help, + workflow_command, + pre_help_text, + post_help_text, + validate_params, + "nextflow_schema.json" + ) + + // + // Check config provided to the pipeline + // + UTILS_NFCORE_PIPELINE ( + nextflow_cli_args + ) + + // + // Custom validation for pipeline parameters + // + validateInputParameters() + +} + +/* +======================================================================================== + SUBWORKFLOW FOR PIPELINE COMPLETION +======================================================================================== +*/ + +workflow PIPELINE_COMPLETION { + + take: + email // string: email address + email_on_fail // string: email address sent on pipeline failure + plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published + monochrome_logs // boolean: Disable ANSI colour codes in log output + hook_url // string: hook URL for notifications + multiqc_report // string: Path to MultiQC report + + main: + + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + + // + // Completion email and summary + // + workflow.onComplete { + if (email || email_on_fail) { + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + } + + completionSummary(monochrome_logs) + + if (hook_url) { + imNotification(summary_params, hook_url) + } + } +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Function to validate channels from input samplesheet +// +def validateInputSamplesheet(input) { + def (metas, fastqs) = input[1..2] + + // Check that multiple runs of the same sample are of the same strandedness + def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1 + if (!strandedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must have the same strandedness!: ${metas[0].id}") + } + + // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + if (!endedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + } + + return [ metas[0], fastqs ] +} + +// +// Check and validate pipeline parameters +// +def validateInputParameters() { + + genomeExistsError() +} + +// +// Get attribute from genome config file e.g. fasta +// +def getGenomeAttribute(attribute) { + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + return params.genomes[ params.genome ][ attribute ] + } + } + return null +} + +// +// Exit pipeline if incorrect --genome key provided +// +def genomeExistsError() { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } +} + +// +// Generate methods description for MultiQC +// +def toolCitationText() { + // TODO nf-core: Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text +} + +def toolBibliographyText() { + // TODO nf-core: Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text +} + +def methodsDescriptionText(mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = workflow.toMap() + meta["manifest_map"] = workflow.manifest.toMap() + + // Pipeline DOI + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + // meta["tool_bibliography"] = toolBibliographyText() + def methods_text = mqc_methods_yaml.text + + def engine = new groovy.text.SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html.toString() +} + +// +// Function to generate an error if contigs in genome fasta file > 512 Mbp +// +def checkMaxContigSize(fai_file) { + def max_size = 512000000 + fai_file.eachLine { line -> + def lspl = line.split('\t') + def chrom = lspl[0] + def size = lspl[1] + if (size.toInteger() > max_size) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Contig longer than ${max_size}bp found in reference genome!\n\n" + + " ${chrom}: ${size}\n\n" + + " Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.\n\n" + + " Please see:\n" + + " https://github.com/nf-core/rnaseq/issues/744\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } + } +} + +// +// Create MultiQC tsv custom content from a list of values +// +def multiqcTsvFromList(tsv_data, header) { + def tsv_string = "" + if (tsv_data.size() > 0) { + tsv_string += "${header.join('\t')}\n" + tsv_string += tsv_data.join('\n') + } + return tsv_string +} + + +// +// Function that parses and returns the alignment rate from the STAR log output +// +def getStarPercentMapped(params, align_log) { + def percent_aligned = 0 + def pattern = /Uniquely mapped reads %\s*\|\s*([\d\.]+)%/ + align_log.eachLine { line -> + def matcher = line =~ pattern + if (matcher) { + percent_aligned = matcher[0][1].toFloat() + } + } + + def pass = false + if (percent_aligned >= params.min_mapped_reads.toFloat()) { + pass = true + } + return [ percent_aligned, pass ] +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf new file mode 100644 index 00000000..ac31f28f --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -0,0 +1,126 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NEXTFLOW_PIPELINE { + + take: + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results + check_conda_channels // boolean: check conda channels + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && outdir) { + dumpParametersToJSON(outdir) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } + + emit: + dummy_emit = true +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(outdir) { + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = JsonOutput.toJson(params) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + Yaml parser = new Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } + + if (channels_missing | channel_priority_violation) { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml new file mode 100644 index 00000000..e5c3a0a8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -0,0 +1,38 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NEXTFLOW_PIPELINE" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" + - "@drpatelh" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..68718e4f --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -0,0 +1,54 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assertAll( + { assert function.success } + ) + } + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..e3f0baf4 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,20 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "v9.9.9" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" + }, + "Test Function checkCondaChannels": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..ca964ce8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,111 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NEXTFLOW_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + workflow "UTILS_NEXTFLOW_PIPELINE" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Should run no inputs") { + + when { + workflow { + """ + print_version = false + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should print version") { + + when { + workflow { + """ + print_version = true + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } + ) + } + } + + test("Should dump params") { + + when { + workflow { + """ + print_version = false + dump_parameters = true + outdir = 'results' + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should not create params JSON if no output directory") { + + when { + workflow { + """ + print_version = false + dump_parameters = true + outdir = null + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config new file mode 100644 index 00000000..d0a926bf --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml new file mode 100644 index 00000000..f8476112 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nextflow_pipeline: + - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf new file mode 100644 index 00000000..a8b55d6f --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -0,0 +1,440 @@ +// +// Subworkflow with utility functions specific to the nf-core pipeline template +// + +import org.yaml.snakeyaml.Yaml +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFCORE_PIPELINE { + + take: + nextflow_cli_args + + main: + valid_config = checkConfigProvided() + checkProfileProvided(nextflow_cli_args) + + emit: + valid_config +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Warn if a -profile or Nextflow config has not been provided to run the pipeline +// +def checkConfigProvided() { + valid_config = true + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + valid_config = false + } + return valid_config +} + +// +// Exit pipeline if --profile contains spaces +// +def checkProfileProvided(nextflow_cli_args) { + if (workflow.profile.endsWith(',')) { + error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } + if (nextflow_cli_args[0]) { + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } +} + +// +// Citation string for pipeline +// +def workflowCitation() { + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + " ${workflow.manifest.doi}\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" +} + +// +// Generate workflow version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + Yaml yaml = new Yaml() + versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + $workflow.manifest.name: ${getWorkflowVersion()} + Nextflow: $workflow.nextflow.version + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions + .unique() + .map { processVersionsFromYAML(it) } + .unique() + .mix(Channel.of(workflowVersionToYAML())) +} + +// +// Get workflow summary for MultiQC +// +def paramsSummaryMultiqc(summary_params) { + def summary_section = '' + for (group in summary_params.keySet()) { + def group_params = summary_params.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    $group

    \n" + summary_section += "
    \n" + for (param in group_params.keySet()) { + summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + + return yaml_file_text +} + +// +// nf-core logo +// +def nfCoreLogo(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} + +// +// Return dashed line +// +def dashedLine(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + +// +// ANSII colours used for terminal logging +// +def logColours(monochrome_logs=true) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// +// Attach the multiqc report to email +// +def attachMultiqcReport(multiqc_report) { + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + if (multiqc_report) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + } + return mqc_report +} + +// +// Construct and send completion email +// +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + + // Set up the e-mail variables + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + if (!workflow.success) { + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + } + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = getWorkflowVersion() + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = attachMultiqcReport(multiqc_report) + + // Check if we are only sending emails on failure + def email_address = email + if (!email && email_on_fail && !workflow.success) { + email_address = email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("${workflow.projectDir}/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("${workflow.projectDir}/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + Map colors = logColours(monochrome_logs) + if (email_address) { + try { + if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { + // Catch failures and try with plaintext + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + mail_cmd.execute() << email_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + } + } + + // Write summary e-mail HTML to a file + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() +} + +// +// Print pipeline summary on completion +// +def completionSummary(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params, hook_url) { + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = getWorkflowVersion() + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml new file mode 100644 index 00000000..d08d2434 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -0,0 +1,24 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PIPELINE" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - nextflow_cli_args: + type: list + description: | + Nextflow CLI positional arguments +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..1dc317f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -0,0 +1,134 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function checkProfileProvided") { + + function "checkProfileProvided" + + when { + function { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function workflowCitation") { + + function "workflowCitation" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function nfCoreLogo") { + + function "nfCoreLogo" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dashedLine") { + + function "dashedLine" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function without logColours") { + + function "logColours" + + when { + function { + """ + input[0] = true + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function with logColours") { + function "logColours" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..1037232c --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,166 @@ +{ + "Test Function checkProfileProvided": { + "content": null, + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" + }, + "Test Function checkConfigProvided": { + "content": [ + true + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" + }, + "Test Function nfCoreLogo": { + "content": [ + "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:10.562934" + }, + "Test Function workflowCitation": { + "content": [ + "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" + }, + "Test Function without logColours": { + "content": [ + { + "reset": "", + "bold": "", + "dim": "", + "underlined": "", + "blink": "", + "reverse": "", + "hidden": "", + "black": "", + "red": "", + "green": "", + "yellow": "", + "blue": "", + "purple": "", + "cyan": "", + "white": "", + "bblack": "", + "bred": "", + "bgreen": "", + "byellow": "", + "bblue": "", + "bpurple": "", + "bcyan": "", + "bwhite": "", + "ublack": "", + "ured": "", + "ugreen": "", + "uyellow": "", + "ublue": "", + "upurple": "", + "ucyan": "", + "uwhite": "", + "iblack": "", + "ired": "", + "igreen": "", + "iyellow": "", + "iblue": "", + "ipurple": "", + "icyan": "", + "iwhite": "", + "biblack": "", + "bired": "", + "bigreen": "", + "biyellow": "", + "biblue": "", + "bipurple": "", + "bicyan": "", + "biwhite": "" + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" + }, + "Test Function dashedLine": { + "content": [ + "-\u001b[2m----------------------------------------------------\u001b[0m-" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" + }, + "Test Function with logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..8940d32d --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap new file mode 100644 index 00000000..859d1030 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -0,0 +1,19 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config new file mode 100644 index 00000000..d0a926bf --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml new file mode 100644 index 00000000..ac8523c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfcore_pipeline: + - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf new file mode 100644 index 00000000..2585b65d --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -0,0 +1,62 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp } from 'plugin/nf-validation' +include { paramsSummaryLog } from 'plugin/nf-validation' +include { validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFVALIDATION_PLUGIN { + + take: + print_help // boolean: print help + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // boolean: validate parameters + schema_filename // path: JSON schema file, null to use default value + + main: + + log.debug "Using schema file: ${schema_filename}" + + // Default values for strings + pre_help_text = pre_help_text ?: '' + post_help_text = post_help_text ?: '' + workflow_command = workflow_command ?: '' + + // + // Print help message if needed + // + if (print_help) { + log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters(parameters_schema: schema_filename) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml new file mode 100644 index 00000000..3d4a6b04 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml @@ -0,0 +1,44 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFVALIDATION_PLUGIN" +description: Use nf-validation to initiate and validate a pipeline +keywords: + - utility + - pipeline + - initialise + - validation +components: [] +input: + - print_help: + type: boolean + description: | + Print help message and exit + - workflow_command: + type: string + description: | + The command to run the workflow e.g. "nextflow run main.nf" + - pre_help_text: + type: string + description: | + Text to print before the help message + - post_help_text: + type: string + description: | + Text to print after the help message + - validate_params: + type: boolean + description: | + Validate the parameters and error if invalid. + - schema_filename: + type: string + description: | + The filename of the schema to validate against. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test new file mode 100644 index 00000000..5784a33f --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -0,0 +1,200 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFVALIDATION_PLUGIN" + script "../main.nf" + workflow "UTILS_NFVALIDATION_PLUGIN" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "plugin/nf-validation" + tag "'plugin/nf-validation'" + tag "utils_nfvalidation_plugin" + tag "subworkflows/utils_nfvalidation_plugin" + + test("Should run nothing") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should run help") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with command") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with extra text") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = "pre-help-text" + post_help_text = "post-help-text" + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('pre-help-text') } }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } }, + { assert workflow.stdout.any { it.contains('post-help-text') } } + ) + } + } + + test("Should validate params") { + + when { + + params { + monochrome_logs = true + test_data = '' + outdir = 1 + } + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = true + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json new file mode 100644 index 00000000..7626c1c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "definitions": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml new file mode 100644 index 00000000..60b1cfff --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfvalidation_plugin: + - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 1cdc6bfb..d3a1d114 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -17,6 +17,8 @@ WorkflowRnafusion.initialise(params, log) // Check mandatory parameters + +//TODO: move this to utils_nf_core_rnafusion_pipeline if (file(params.input).exists() || params.build_references) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet does not exist or was not specified!' } if (params.fusioninspector_only && !params.fusioninspector_fusions) { exit 1, 'Parameter --fusioninspector_fusions PATH_TO_FUSION_LIST expected with parameter --fusioninspector_only'} if (params.tools_cutoff < 1) { exit 1, 'Parameter: --tools_cutoff should be >= 1'} @@ -88,6 +90,8 @@ include { FUSIONCATCHER_WORKFLOW } from '../subworkflows/local/fusionca include { FUSIONINSPECTOR_WORKFLOW } from '../subworkflows/local/fusioninspector_workflow' include { FUSIONREPORT_WORKFLOW } from '../subworkflows/local/fusionreport_workflow' +include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_rnaseq_pipeline' + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT NF-CORE MODULES/SUBWORKFLOWS @@ -118,31 +122,35 @@ workflow RNAFUSION { ch_versions = Channel.empty() - - // - // SUBWORKFLOW: Read in samplesheet, validate and stage input files + // Create channel from input file provided through params.input // - INPUT_CHECK ( - file(params.input) - ) - .reads - .map { - meta, fastq -> - def meta_clone = meta.clone() - meta_clone.id = meta_clone.id.split('_')[0..-2].join('_') - [ meta_clone, fastq ] } - .groupTuple(by: [0]) - .branch { - meta, fastq -> - single : fastq.size() == 1 - return [ meta, fastq.flatten() ] - multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] - } - .set { ch_fastq } - ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + Channel + .fromSamplesheet("input") + .map { + meta, fastq_1, fastq_2 -> + if (!fastq_2) { + return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { + validateInputSamplesheet(it) + } + .branch { + meta, fastqs -> + single : fastqs.size() == 1 + return [ meta, fastqs.flatten() ] + multiple: fastqs.size() > 1 + return [ meta, fastqs.flatten() ] + } + .set { ch_fastq } + // + // MODULE: Concatenate FastQ files from same sample if required + // CAT_FASTQ ( ch_fastq.multiple ) @@ -167,7 +175,10 @@ workflow RNAFUSION { ch_reads_all = TRIM_WORKFLOW.out.ch_reads_all ch_versions = ch_versions.mix(TRIM_WORKFLOW.out.versions) - // Run STAR alignment and Arriba + // + // SUBWORKFLOW: Run STAR alignment and Arriba + // + ARRIBA_WORKFLOW ( ch_reads_all, ch_gtf, From 3e8a300b11bdf2085fd4f16a1b9e91daf10394a9 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 13:28:37 +0100 Subject: [PATCH 04/28] first changes --- main.nf | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/main.nf b/main.nf index 3a8dfc57..396ae487 100644 --- a/main.nf +++ b/main.nf @@ -13,17 +13,25 @@ nextflow.enable.dsl = 2 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') -params.fai = WorkflowMain.getGenomeAttribute(params, 'fai') -params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf') -params.chrgtf = WorkflowMain.getGenomeAttribute(params, 'chrgtf') -params.transcript = WorkflowMain.getGenomeAttribute(params, 'transcript') -params.refflat = WorkflowMain.getGenomeAttribute(params, 'refflat') -params.rrna_intervals = WorkflowMain.getGenomeAttribute(params, 'rrna_intervals') +include { BUILD_REFERENCES } from './workflows/build_references' +include { RNAFUSION } from './workflows/rnafusion' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnafusion_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_rnafusion_pipeline' +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_rnafusion_pipeline' + + + +params.fasta = getGenomeAttribute('fasta') +params.fai = getGenomeAttribute('fai') +params.gtf = getGenomeAttribute('gtf') +params.chrgtf = getGenomeAttribute('chrgtf') +params.transcript = getGenomeAttribute('transcript') +params.refflat = getGenomeAttribute('refflat') +params.rrna_intervals = getGenomeAttribute('rrna_intervals') /* ======================================================================================== From ef0ac08e843fc6f4d1fe6188263409c2b3a00b4d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 15:01:32 +0100 Subject: [PATCH 05/28] remove genome arg --- nextflow_schema.json | 5 ----- 1 file changed, 5 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 2a311296..5beb02f0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -284,11 +284,6 @@ "fa_icon": "fas fa-dna", "description": "Reference genome related files and options required for the workflow.", "properties": { - "genome": { - "type": "string", - "description": "Name of iGenomes reference.", - "fa_icon": "fas fa-book" - }, "fasta": { "type": "string", "format": "file-path", From 7f37d02631a0de542246221e6f184c422b38b153 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 15:04:47 +0100 Subject: [PATCH 06/28] move fasta out from genome --- conf/genomes.config | 23 ----------------------- nextflow.config | 15 +++++++++++---- 2 files changed, 11 insertions(+), 27 deletions(-) delete mode 100644 conf/genomes.config diff --git a/conf/genomes.config b/conf/genomes.config deleted file mode 100644 index c1385ebe..00000000 --- a/conf/genomes.config +++ /dev/null @@ -1,23 +0,0 @@ -/* - * ------------------------------------------------- - * Nextflow config file for reference genome - * ------------------------------------------------- - * These references have to be build manually due - * to ERCC spike-ins. - * Can be used by any config that customizes the base - * path using $params.genomes_base / --genomes_base - */ - -params { - genomes { - 'GRCh38' { - fasta = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa" - fai = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa.fai" - gtf = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.gtf" - chrgtf = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.chr.gtf" - transcript = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.cdna.all.fa.gz" - refflat = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.chr.gtf.refflat" - rrna_intervals= "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.interval_list" - } - } -} diff --git a/nextflow.config b/nextflow.config index d2352a8c..8eca3ca0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,6 +16,8 @@ params { cosmic_passwd = null qiagen = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -24,13 +26,21 @@ params { multiqc_methods_description = null // Genome - genome = 'GRCh38' genomes_base = "${params.outdir}/references" ensembl_version = 102 read_length = 100 genomes = [:] starfusion_build = true + // Genomes options + fasta = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa" + fai = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa.fai" + gtf = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.gtf" + chrgtf = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.chr.gtf" + transcript = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.cdna.all.fa.gz" + refflat = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.chr.gtf.refflat" + rrna_intervals= "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.interval_list" + // Filtering tools_cutoff = 1 @@ -114,7 +124,6 @@ params { // Schema validation default options validationFailUnrecognisedParams = false validationLenientMode = false - validationSchemaIgnoreParams = 'genomes' validationShowHiddenParams = false validate_params = true } @@ -122,8 +131,6 @@ params { // Load base.config by default for all pipelines includeConfig 'conf/base.config' -includeConfig 'conf/genomes.config' - // Load nf-core custom profiles from different Institutions try { includeConfig "${params.custom_config_base}/nfcore_custom.config" From 49d4ecaf1448af8352b6c31d6bd7089e33337e5b Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 15:16:12 +0100 Subject: [PATCH 07/28] merge fixes --- conf/base.config | 3 --- conf/modules.config | 8 -------- modules.json | 24 ------------------------ nextflow.config | 1 - 4 files changed, 36 deletions(-) diff --git a/conf/base.config b/conf/base.config index 165a5e88..5b2e6f36 100644 --- a/conf/base.config +++ b/conf/base.config @@ -52,7 +52,4 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - } } diff --git a/conf/modules.config b/conf/modules.config index fb0be54e..5bd32d63 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -49,14 +49,6 @@ process { ] } - withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } - withName: 'ENSEMBL_DOWNLOAD' { publishDir = [ path: { "${params.genomes_base}/ensembl" }, diff --git a/modules.json b/modules.json index 4fef058f..23a6ce29 100644 --- a/modules.json +++ b/modules.json @@ -25,11 +25,6 @@ "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] - }, "fastp": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", @@ -112,25 +107,6 @@ } } }, - "subworkflows": { - "nf-core": { - "utils_nextflow_pipeline": { - "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] - }, - "utils_nfcore_pipeline": { - "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] - }, - "utils_nfvalidation_plugin": { - "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] - } - } - }, "subworkflows": { "nf-core": { "utils_nextflow_pipeline": { diff --git a/nextflow.config b/nextflow.config index 8eca3ca0..0341ae61 100644 --- a/nextflow.config +++ b/nextflow.config @@ -29,7 +29,6 @@ params { genomes_base = "${params.outdir}/references" ensembl_version = 102 read_length = 100 - genomes = [:] starfusion_build = true // Genomes options From b64f5ae32fa2886e883ef3aa06c0809f4e685d31 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 15:17:25 +0100 Subject: [PATCH 08/28] merge fixes --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 0341ae61..632565ee 100644 --- a/nextflow.config +++ b/nextflow.config @@ -123,6 +123,7 @@ params { // Schema validation default options validationFailUnrecognisedParams = false validationLenientMode = false + validationSchemaIgnoreParams = '' validationShowHiddenParams = false validate_params = true } From 296bb48a05cf27a9f7741caebdb8d3890d381e91 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 15:48:23 +0100 Subject: [PATCH 09/28] genomes --- nextflow.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 632565ee..45d63730 100644 --- a/nextflow.config +++ b/nextflow.config @@ -30,6 +30,7 @@ params { ensembl_version = 102 read_length = 100 starfusion_build = true + genomes = [:] // Genomes options fasta = "${params.genomes_base}/ensembl/Homo_sapiens.${params.genome}.${params.ensembl_version}.all.fa" @@ -123,7 +124,7 @@ params { // Schema validation default options validationFailUnrecognisedParams = false validationLenientMode = false - validationSchemaIgnoreParams = '' + validationSchemaIgnoreParams = 'genomes' validationShowHiddenParams = false validate_params = true } From f551306d2af946b1f0c4c72f6e8e0b62e69a4852 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 15:54:32 +0100 Subject: [PATCH 10/28] add genome --- nextflow.config | 1 + nextflow_schema.json | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/nextflow.config b/nextflow.config index 45d63730..3c22cd82 100644 --- a/nextflow.config +++ b/nextflow.config @@ -26,6 +26,7 @@ params { multiqc_methods_description = null // Genome + genome = 'GRCh38' genomes_base = "${params.outdir}/references" ensembl_version = 102 read_length = 100 diff --git a/nextflow_schema.json b/nextflow_schema.json index 5beb02f0..2a311296 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -284,6 +284,11 @@ "fa_icon": "fas fa-dna", "description": "Reference genome related files and options required for the workflow.", "properties": { + "genome": { + "type": "string", + "description": "Name of iGenomes reference.", + "fa_icon": "fas fa-book" + }, "fasta": { "type": "string", "format": "file-path", From 38fe79f92279fd3fa39ed4ff459bcda8d329f263 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 17:52:04 +0100 Subject: [PATCH 11/28] fix merging --- main.nf | 9 +--- .../utils_nfcore_rnafusion_pipeline/main.nf | 29 +---------- workflows/build_references.nf | 12 ++--- workflows/rnafusion.nf | 48 +++++++------------ 4 files changed, 28 insertions(+), 70 deletions(-) diff --git a/main.nf b/main.nf index 76253a91..6fe53192 100644 --- a/main.nf +++ b/main.nf @@ -35,9 +35,6 @@ include { RNAFUSION } from './workflows/rnafusion' // workflow NFCORE_RNAFUSION { - take: - samplesheet // channel: samplesheet read in from --input - main: // @@ -46,7 +43,7 @@ workflow NFCORE_RNAFUSION { if (params.build_references) { BUILD_REFERENCES () } else { - RNAFUSION(samplesheet) + RNAFUSION() } emit: @@ -79,9 +76,7 @@ workflow { // // WORKFLOW: Run main workflow // - NFCORE_RNAFUSION ( - PIPELINE_INITIALISATION.out.samplesheet - ) + NFCORE_RNAFUSION () // // SUBWORKFLOW: Run completion tasks diff --git a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf index a60d3f6b..98b9d7e7 100644 --- a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf @@ -2,6 +2,8 @@ // Subworkflow with functionality specific to the nf-core/rnafusion pipeline // +import groovy.json.JsonSlurper + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS @@ -79,33 +81,6 @@ workflow PIPELINE_INITIALISATION { // validateInputParameters() - // - // Create channel from input file provided through params.input - // - Channel - .fromSamplesheet("input") - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() - .map { - validateInputSamplesheet(it) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } - .set { ch_samplesheet } - - emit: - samplesheet = ch_samplesheet - versions = ch_versions - } /* diff --git a/workflows/build_references.nf b/workflows/build_references.nf index 0ebf3c08..cfbafafe 100644 --- a/workflows/build_references.nf +++ b/workflows/build_references.nf @@ -86,12 +86,12 @@ workflow BUILD_REFERENCES { ======================================================================================== */ -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.summary(workflow, params, log) -} +// workflow.onComplete { +// if (params.email || params.email_on_fail) { +// NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) +// } +// NfcoreTemplate.summary(workflow, params, log) +// } /* ======================================================================================== diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index c97761e2..98345287 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -6,7 +6,6 @@ include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnafusion_pipeline' @@ -24,22 +23,22 @@ include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' // if (params.tools_cutoff < 1) { exit 1, 'Parameter: --tools_cutoff should be >= 1'} -// ch_chrgtf = params.starfusion_build ? Channel.fromPath(params.chrgtf).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_annot.gtf").map { it -> [[id:it.Name], it] }.collect() -// ch_starindex_ref = params.starfusion_build ? Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_genome.fa.star.idx").map { it -> [[id:it.Name], it] }.collect() -// ch_starindex_ensembl_ref = Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() -// ch_refflat = params.starfusion_build ? Channel.fromPath(params.refflat).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.gtf.refflat").map { it -> [[id:it.Name], it] }.collect() -// ch_rrna_interval = params.starfusion_build ? Channel.fromPath(params.rrna_intervals).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.interval_list").map { it -> [[id:it.Name], it] }.collect() -// ch_fusionreport_ref = Channel.fromPath(params.fusionreport_ref).map { it -> [[id:it.Name], it] }.collect() -// ch_arriba_ref_blacklist = Channel.fromPath(params.arriba_ref_blacklist).map { it -> [[id:it.Name], it] }.collect() -// ch_arriba_ref_known_fusions = Channel.fromPath(params.arriba_ref_known_fusions).map { it -> [[id:it.Name], it] }.collect() -// ch_arriba_ref_protein_domains = Channel.fromPath(params.arriba_ref_protein_domains).map { it -> [[id:it.Name], it] }.collect() -// ch_arriba_ref_cytobands = Channel.fromPath(params.arriba_ref_cytobands).map { it -> [[id:it.Name], it] }.collect() -// ch_hgnc_ref = Channel.fromPath(params.hgnc_ref).map { it -> [[id:it.Name], it] }.collect() -// ch_hgnc_date = Channel.fromPath(params.hgnc_date).map { it -> [[id:it.Name], it] }.collect() -// ch_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it.Name], it] }.collect() -// ch_gtf = Channel.fromPath(params.gtf).map { it -> [[id:it.Name], it] }.collect() -// ch_transcript = Channel.fromPath(params.transcript).map { it -> [[id:it.Name], it] }.collect() -// ch_fai = Channel.fromPath(params.fai).map { it -> [[id:it.Name], it] }.collect() +ch_chrgtf = params.starfusion_build ? Channel.fromPath(params.chrgtf).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_annot.gtf").map { it -> [[id:it.Name], it] }.collect() +ch_starindex_ref = params.starfusion_build ? Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_genome.fa.star.idx").map { it -> [[id:it.Name], it] }.collect() +ch_starindex_ensembl_ref = Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() +ch_refflat = params.starfusion_build ? Channel.fromPath(params.refflat).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.gtf.refflat").map { it -> [[id:it.Name], it] }.collect() +ch_rrna_interval = params.starfusion_build ? Channel.fromPath(params.rrna_intervals).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.interval_list").map { it -> [[id:it.Name], it] }.collect() +ch_fusionreport_ref = Channel.fromPath(params.fusionreport_ref).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_blacklist = Channel.fromPath(params.arriba_ref_blacklist).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_known_fusions = Channel.fromPath(params.arriba_ref_known_fusions).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_protein_domains = Channel.fromPath(params.arriba_ref_protein_domains).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_cytobands = Channel.fromPath(params.arriba_ref_cytobands).map { it -> [[id:it.Name], it] }.collect() +ch_hgnc_ref = Channel.fromPath(params.hgnc_ref).map { it -> [[id:it.Name], it] }.collect() +ch_hgnc_date = Channel.fromPath(params.hgnc_date).map { it -> [[id:it.Name], it] }.collect() +ch_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it.Name], it] }.collect() +ch_gtf = Channel.fromPath(params.gtf).map { it -> [[id:it.Name], it] }.collect() +ch_transcript = Channel.fromPath(params.transcript).map { it -> [[id:it.Name], it] }.collect() +ch_fai = Channel.fromPath(params.fai).map { it -> [[id:it.Name], it] }.collect() // def checkPathParamList = [ // params.fasta, @@ -70,7 +69,6 @@ include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { INPUT_CHECK } from '../subworkflows/local/input_check' include { TRIM_WORKFLOW } from '../subworkflows/local/trim_workflow' include { ARRIBA_WORKFLOW } from '../subworkflows/local/arriba_workflow' include { QC_WORKFLOW } from '../subworkflows/local/qc_workflow' @@ -79,7 +77,7 @@ include { STRINGTIE_WORKFLOW } from '../subworkflows/local/stringti include { FUSIONCATCHER_WORKFLOW } from '../subworkflows/local/fusioncatcher_workflow' include { FUSIONINSPECTOR_WORKFLOW } from '../subworkflows/local/fusioninspector_workflow' include { FUSIONREPORT_WORKFLOW } from '../subworkflows/local/fusionreport_workflow' -include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_rnaseq_pipeline' +include { validateInputSamplesheet } from '../subworkflows/local/utils_nfcore_rnafusion_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -91,9 +89,6 @@ include { validateInputSamplesheet } from '../../subworkflows/local/utils_n // MODULE: Installed directly from nf-core/modules // include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -103,9 +98,6 @@ include { MULTIQC } from '../modules/nf-core/multiqc/main' workflow RNAFUSION { - take: - ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() @@ -152,15 +144,11 @@ workflow RNAFUSION { // MODULE: Run FastQC // FASTQC ( - ch_samplesheet + ch_cat_fastq ) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - ch_cat_fastq - ) - ch_versions = ch_versions.mix(FASTQC.out.versions) - TRIM_WORKFLOW ( ch_cat_fastq ) From 3a9e1233be5fe2ab163f80e49b73dac6a72bb4c0 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 18:05:42 +0100 Subject: [PATCH 12/28] fix merging --- main.nf | 4 ---- subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf | 3 +-- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/main.nf b/main.nf index 6fe53192..8ba6f049 100644 --- a/main.nf +++ b/main.nf @@ -46,9 +46,6 @@ workflow NFCORE_RNAFUSION { RNAFUSION() } - emit: - multiqc_report = RNAFUSION.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -88,7 +85,6 @@ workflow { params.outdir, params.monochrome_logs, params.hook_url, - NFCORE_RNAFUSION.out.multiqc_report ) } diff --git a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf index 98b9d7e7..e7d4e72d 100644 --- a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf @@ -98,7 +98,6 @@ workflow PIPELINE_COMPLETION { outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications - multiqc_report // string: Path to MultiQC report main: @@ -109,7 +108,7 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, null) } completionSummary(monochrome_logs) From 22e3ecb163e21e6e32c1394bca71931b84e8ae52 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Mar 2024 20:01:02 +0100 Subject: [PATCH 13/28] checks --- conf/modules.config | 4 ---- nextflow.config | 2 -- workflows/build_references.nf | 13 ------------- workflows/rnafusion.nf | 6 ++---- 4 files changed, 2 insertions(+), 23 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 5bd32d63..9d4ca62b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,10 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: FASTQC { - ext.args = '--quiet' - } - withName: 'ARRIBA' { publishDir = [ path: { "${params.outdir}/arriba" }, diff --git a/nextflow.config b/nextflow.config index 3c22cd82..1a35e3c7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,8 +16,6 @@ params { cosmic_passwd = null qiagen = false - - // MultiQC options multiqc_config = null multiqc_title = null diff --git a/workflows/build_references.nf b/workflows/build_references.nf index cfbafafe..7847dd05 100644 --- a/workflows/build_references.nf +++ b/workflows/build_references.nf @@ -80,19 +80,6 @@ workflow BUILD_REFERENCES { } -/* -======================================================================================== - COMPLETION EMAIL AND SUMMARY -======================================================================================== -*/ - -// workflow.onComplete { -// if (params.email || params.email_on_fail) { -// NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) -// } -// NfcoreTemplate.summary(workflow, params, log) -// } - /* ======================================================================================== THE END diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 98345287..63c2f1f1 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -14,7 +14,7 @@ include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -// // Check mandatory parameters +// Check mandatory parameters // //TODO: move this to utils_nf_core_rnafusion_pipeline @@ -98,8 +98,6 @@ include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' workflow RNAFUSION { - main: - ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() @@ -147,7 +145,7 @@ workflow RNAFUSION { ch_cat_fastq ) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + ch_versions = ch_versions.mix(FASTQC.out.versions) TRIM_WORKFLOW ( ch_cat_fastq From dae6bd1c5f5df9d108c6ad405008bfcc195ed309 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Mar 2024 09:00:48 +0100 Subject: [PATCH 14/28] remove commented out param checks, moved to issue --- workflows/rnafusion.nf | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 63c2f1f1..a1b8f431 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -11,18 +11,6 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnafusion_pipeline' include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' - - - -// Check mandatory parameters - - -// //TODO: move this to utils_nf_core_rnafusion_pipeline -// if (file(params.input).exists() || params.build_references) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet does not exist or was not specified!' } -// if (params.fusioninspector_only && !params.fusioninspector_fusions) { exit 1, 'Parameter --fusioninspector_fusions PATH_TO_FUSION_LIST expected with parameter --fusioninspector_only'} -// if (params.tools_cutoff < 1) { exit 1, 'Parameter: --tools_cutoff should be >= 1'} - - ch_chrgtf = params.starfusion_build ? Channel.fromPath(params.chrgtf).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_annot.gtf").map { it -> [[id:it.Name], it] }.collect() ch_starindex_ref = params.starfusion_build ? Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_genome.fa.star.idx").map { it -> [[id:it.Name], it] }.collect() ch_starindex_ensembl_ref = Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() @@ -40,24 +28,6 @@ ch_gtf = Channel.fromPath(params.gtf).map { it -> [[id:it.Name], it] }.collect() ch_transcript = Channel.fromPath(params.transcript).map { it -> [[id:it.Name], it] }.collect() ch_fai = Channel.fromPath(params.fai).map { it -> [[id:it.Name], it] }.collect() -// def checkPathParamList = [ -// params.fasta, -// params.fai, -// params.gtf, -// params.transcript, -// ] - -// for (param in checkPathParamList) if ((param) && !params.build_references) file(param, checkIfExists: true) -// def params_fasta_path_uri = params.fasta =~ /^([a-zA-Z0-9]*):\/\/(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$/ -// // check if params.fasta is a remote uri such as s3://, gs:// or dx:// -// if (params_fasta_path_uri){ -// log.info "INFO: a remote uri path detected, check for absolute path and trailing '/' not performed" -// // log.info "INFO: remote uri path detected (e.g. s3), check for absolute path and trailing '/' not performed" -// } -// else { -// for (param in checkPathParamList) if ((param.toString())!= file(param).toString() && !params.build_references) { exit 1, "Problem with ${param}: ABSOLUTE PATHS are required! Check for trailing '/' at the end of paths too." } -// } - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From bddbb710becadaa4d0e64e552328acc1fbd432da Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Mar 2024 13:51:11 +0100 Subject: [PATCH 15/28] add strandedness in input schema --- .nf-test.log | 4 ++++ assets/schema_input.json | 9 ++++++++- nf-test.config | 8 ++++++++ tests/main.nf.test | 31 +++++++++++++++++++++++++++++++ 4 files changed, 51 insertions(+), 1 deletion(-) create mode 100644 .nf-test.log create mode 100644 nf-test.config create mode 100644 tests/main.nf.test diff --git a/.nf-test.log b/.nf-test.log new file mode 100644 index 00000000..8da6769a --- /dev/null +++ b/.nf-test.log @@ -0,0 +1,4 @@ +Mar-06 08:33:23.861 [main] INFO com.askimed.nf.test.App - nf-test 0.8.1 +Mar-06 08:33:23.919 [main] INFO com.askimed.nf.test.App - Arguments: [test, --profile, debug,test,docker, --verbose] +Mar-06 08:33:23.924 [main] INFO com.askimed.nf.test.commands.RunTestsCommand - Load config from file /Users/annick.renevey/Projects/rnafusion/nf-test.config... +Mar-06 08:33:24.984 [main] ERROR com.askimed.nf.test.commands.RunTestsCommand - No tests ot directories found containing test files. diff --git a/assets/schema_input.json b/assets/schema_input.json index fa630b6c..12ec2cc8 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -26,8 +26,15 @@ "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + }, + "strandedness": { + "type": "string", + "format": "string", + "exists": true, + "pattern": "forward|reverse|unstranded|unknown", + "errorMessage": "Strandedness has to be forward, reverse, unstranded or unknown" } }, - "required": ["sample", "fastq_1"] + "required": ["sample", "fastq_1", "fastq_2", "strandedness"] } } diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..870799df --- /dev/null +++ b/nf-test.config @@ -0,0 +1,8 @@ +config { + + testsDir "tests" + workDir ".nf-test" + configFile "tests/nextflow.config" + profile "" + +} diff --git a/tests/main.nf.test b/tests/main.nf.test new file mode 100644 index 00000000..25f5c9aa --- /dev/null +++ b/tests/main.nf.test @@ -0,0 +1,31 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnafusion" + + test("Run build references with profile test") { + + when { + params { + build_references = true + outdir = "results" + genome_base = "references" + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' + cosmic_username = secrets.COSMIC_USERNAME + cosmic_passwd = secrets.COSMIC_PASSWD + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + +} From 2c1f1e5c91ace13c2b0448086e627ae8061839a7 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Mar 2024 14:14:48 +0100 Subject: [PATCH 16/28] update instructions to run nf-test --- .github/CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 8e5d1fef..3cfa08b3 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -26,7 +26,7 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command, BUT DON'T FORGET TO ADD THE PARAMETERS cosmic_username AND cosmic_passwd in tests/main.nf.test. ```bash nf-test test --profile debug,test,docker --verbose From 255d91ca95acf9785c6b30f680faee7eef3b4160 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Mar 2024 14:15:02 +0100 Subject: [PATCH 17/28] writh pipeline test --- tests/main.nf.test | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/tests/main.nf.test b/tests/main.nf.test index 25f5c9aa..715335d8 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -16,8 +16,8 @@ nextflow_pipeline { max_memory = '6.GB' max_time = '6.h' input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' - cosmic_username = secrets.COSMIC_USERNAME - cosmic_passwd = secrets.COSMIC_PASSWD + cosmic_username = COSMIC_USERNAME + cosmic_passwd = COSMIC_PASSWD } } @@ -27,5 +27,23 @@ nextflow_pipeline { ) } } + test("Run fusion detection with profile test") { + when { + params { + outdir = "results" + genome_base = "references" + max_cpus = 2 + max_memory = '6.GB' + max_time = '6.h' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } } From ffed4c05c54ec05345a4b1b8cb0506f7aa05de4b Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Mar 2024 14:15:25 +0100 Subject: [PATCH 18/28] write general test config --- tests/nextflow.config | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 tests/nextflow.config diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 00000000..ebd067ac --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,35 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ + +params { + // Base directory for nf-core/modules test data + modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' + + // Base directory for nf-core/rnaseq test data + pipelines_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/' + + outdir = 'results' +} + +// Impose sensible resource limits for testing +process { + withName: '.*' { + cpus = 2 + memory = 3.GB + time = 2.h + } +} + +// Impose same minimum Nextflow version as the pipeline for testing +manifest { + nextflowVersion = '!>=23.04.0' +} + +// Disable all Nextflow reporting options +timeline { enabled = false } +report { enabled = false } +trace { enabled = false } +dag { enabled = false } From 645634c3fc178bb15766502e073c37a8b4de6147 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Mar 2024 14:18:42 +0100 Subject: [PATCH 19/28] comment out nf-test from PR template --- .github/PULL_REQUEST_TEMPLATE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 8b85a0aa..d2824258 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnaf - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnafusion/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/rnafusion _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). + - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. From 6a31fd0d49d48dffe5e9f9cdca3728478cf618da Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Mar 2024 14:56:57 +0100 Subject: [PATCH 20/28] CONTRIBUTING AND PULL_REQUEST_TEMPLATE not part of files_unchanged --- .nf-core.yml | 4 + .../meta/assets | 1 + .../818076bdee20d7e7df39ccd4d6617997/meta/bin | 1 + .../meta/nextflow.log | 314 ++++++++++++++++++ .../meta/params.json | 1 + .../meta/std.err | 0 .../meta/std.out | 145 ++++++++ .../meta/trace.csv | 3 + 8 files changed, 469 insertions(+) create mode 120000 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/assets create mode 120000 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/bin create mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log create mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json create mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.err create mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.out create mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv diff --git a/.nf-core.yml b/.nf-core.yml index 3805dc81..78a3fd2e 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,5 @@ repository_type: pipeline +lint: + files_unchanged: + - .github/CONTRIBUTING.md + - .github/PULL_REQUEST_TEMPLATE.md diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/assets b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/assets new file mode 120000 index 00000000..e4ea7900 --- /dev/null +++ b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/assets @@ -0,0 +1 @@ +/Users/annick.renevey/Projects/rnafusion/assets \ No newline at end of file diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/bin b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/bin new file mode 120000 index 00000000..db857c9f --- /dev/null +++ b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/bin @@ -0,0 +1 @@ +/Users/annick.renevey/Projects/rnafusion/bin \ No newline at end of file diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log new file mode 100644 index 00000000..586050f1 --- /dev/null +++ b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log @@ -0,0 +1,314 @@ +Mar-08 14:13:11.080 [main] DEBUG nextflow.cli.Launcher - $> nextflow -log /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log run /Users/annick.renevey/Projects/rnafusion/tests/../main.nf -c /Users/annick.renevey/Projects/rnafusion/nextflow.config -c /Users/annick.renevey/Projects/rnafusion/tests/nextflow.config -params-file /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json -ansi-log false -profile debug,test,docker -with-trace /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv -w /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work +Mar-08 14:13:11.190 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.1 +Mar-08 14:13:11.228 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2 +Mar-08 14:13:11.245 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] +Mar-08 14:13:11.246 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] +Mar-08 14:13:11.250 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode +Mar-08 14:13:11.269 [main] INFO org.pf4j.AbstractPluginManager - No plugins +Mar-08 14:13:11.303 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/rnafusion/nextflow.config +Mar-08 14:13:11.310 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/rnafusion/nextflow.config +Mar-08 14:13:11.311 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/rnafusion/tests/nextflow.config +Mar-08 14:13:11.311 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/rnafusion/nextflow.config +Mar-08 14:13:11.311 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/rnafusion/nextflow.config +Mar-08 14:13:11.311 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/rnafusion/tests/nextflow.config +Mar-08 14:13:11.393 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `debug,test,docker` +Mar-08 14:13:16.099 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `debug,test,docker` +Mar-08 14:13:17.277 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `debug,test,docker` +Mar-08 14:13:17.413 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, imperial, maestro, software_license, utd_europa, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, ethz_euler, test_full, imb, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] +Mar-08 14:13:17.512 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion +Mar-08 14:13:17.534 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/rnafusion/tests/../main.nf` [cheesy_hawking] DSL2 - revision: 12cef51b71 +Mar-08 14:13:17.536 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation@1.1.3] +Mar-08 14:13:17.541 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] +Mar-08 14:13:17.541 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation@1.1.3] +Mar-08 14:13:17.542 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3 +Mar-08 14:13:17.559 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved +Mar-08 14:13:17.560 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3' +Mar-08 14:13:17.592 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3 +Mar-08 14:13:17.616 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json +Mar-08 14:13:17.628 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@57e03347] - activable => nextflow.secret.LocalSecretsProvider@57e03347 +Mar-08 14:13:17.713 [main] DEBUG nextflow.Session - Session UUID: 1bbe00d2-1928-4556-b97c-ecef4af4222e +Mar-08 14:13:17.713 [main] DEBUG nextflow.Session - Run name: cheesy_hawking +Mar-08 14:13:17.714 [main] DEBUG nextflow.Session - Executor pool size: 8 +Mar-08 14:13:17.727 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false +Mar-08 14:13:17.787 [main] DEBUG nextflow.cli.CmdRun - + Version: 23.04.1 build 5866 + Created: 15-04-2023 06:51 UTC (08:51 CEST) + System: Mac OS X 14.2.1 + Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS + Encoding: UTF-8 (UTF-8) + Process: 89543@annickrmbp [130.229.140.244] + CPUs: 8 - Mem: 16 GB (22.8 MB) - Swap: 6 GB (1.4 GB) +Mar-08 14:13:17.818 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work [Mac OS X] +Mar-08 14:13:17.840 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] +Mar-08 14:13:17.857 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory +Mar-08 14:13:17.959 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory +Mar-08 14:13:17.990 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 +Mar-08 14:13:18.140 [main] DEBUG nextflow.Session - Session start +Mar-08 14:13:18.175 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv +Mar-08 14:13:18.579 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution +Mar-08 14:13:19.365 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation +Mar-08 14:13:19.385 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation +Mar-08 14:13:19.385 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation +Mar-08 14:13:19.411 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation +Mar-08 14:13:19.413 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation +Mar-08 14:13:22.583 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation +Mar-08 14:13:22.586 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation +Mar-08 14:13:22.586 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation +Mar-08 14:13:22.588 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation +Mar-08 14:13:22.588 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation +Mar-08 14:13:22.738 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation +Mar-08 14:13:27.381 [main] DEBUG nextflow.Nextflow - Using schema file: nextflow_schema.json +Mar-08 14:13:27.389 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` +Mar-08 14:13:27.418 [main] INFO nextflow.Nextflow - + +------------------------------------------------------ + ,--./,-. + ___ __ __ __ ___ /,-._.--~' + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + nf-core/rnafusion v3.0.2dev +------------------------------------------------------ +Core Nextflow options + runName : cheesy_hawking + containerEngine : docker + launchDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997 + workDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work + projectDir : /Users/annick.renevey/Projects/rnafusion + userName : annick.renevey + profile : debug,test,docker + configFiles :  + +Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv + outdir : results + build_references : true + genomes_base : results/references + starfusion_build : true + arriba_ref : results/references/arriba + arriba_ref_blacklist : results/references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz + arriba_ref_cytobands : results/references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv + arriba_ref_known_fusions : results/references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz + arriba_ref_protein_domains : results/references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3 + ensembl_ref : results/references/ensembl + fusioncatcher_limitSjdbInsertNsj : 2000000 + fusioncatcher_ref : results/references/fusioncatcher/human_v102 + fusioninspector_limitSjdbInsertNsj: 1000000 + fusionreport_ref : results/references/fusion_report_db + hgnc_ref : results/references/hgnc/hgnc_complete_set.txt + hgnc_date : results/references/hgnc/HGNC-DB-timestamp.txt + starfusion_ref : results/references/starfusion/ctat_genome_lib_build_dir + starindex_ref : results/references/star + tools_cutoff : 1 + +Read trimming options + adapter_fasta : [] + +Alignment compression options + cram : [] + +Reference genome options + genome : GRCh38 + fasta : results/references/ensembl/Homo_sapiens.GRCh38.102.all.fa + fai : results/references/ensembl/Homo_sapiens.GRCh38.102.all.fa.fai + gtf : results/references/ensembl/Homo_sapiens.GRCh38.102.gtf + chrgtf : results/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf + transcript : results/references/ensembl/Homo_sapiens.GRCh38.102.cdna.all.fa.gz + refflat : results/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf.refflat + rrna_intervals : results/references/ensembl/Homo_sapiens.GRCh38.102.interval_list + +Institutional config options + config_profile_name : Test profile + config_profile_description : Minimal test dataset to check pipeline function + +Max job request options + max_cpus : 2 + max_memory : 6.GB + max_time : 6.h + +!! Only displaying parameters that differ from the pipeline defaults !! +------------------------------------------------------ +If you use nf-core/rnafusion for your analysis please cite: + +* The pipeline + + +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md +------------------------------------------------------ +Mar-08 14:13:27.425 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation +Mar-08 14:13:27.617 [main] WARN nextflow.validation.SchemaValidator - The following invalid input values have been detected: + +* --genome_base: references +* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/ +* --pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/ + + +Mar-08 14:13:27.912 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' with '/Users/annick.renevey/Projects/rnafusion/assets/schema_input.json' +Mar-08 14:13:29.935 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' with '/Users/annick.renevey/Projects/rnafusion/assets/schema_input.json' +Mar-08 14:13:29.935 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation +Mar-08 14:13:30.046 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD +Mar-08 14:13:30.049 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ENSEMBL_DOWNLOAD` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD +Mar-08 14:13:30.050 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD +Mar-08 14:13:30.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD +Mar-08 14:13:30.061 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +Mar-08 14:13:30.061 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +Mar-08 14:13:30.083 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local +Mar-08 14:13:30.090 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=16 GB; capacity=8; pollInterval=100ms; dumpInterval=5m +Mar-08 14:13:30.203 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD +Mar-08 14:13:30.204 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:HGNC_DOWNLOAD` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD +Mar-08 14:13:30.206 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD +Mar-08 14:13:30.207 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD +Mar-08 14:13:30.213 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +Mar-08 14:13:30.214 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +Mar-08 14:13:30.236 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX +Mar-08 14:13:30.237 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX +Mar-08 14:13:30.238 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX +Mar-08 14:13:30.238 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX +Mar-08 14:13:30.240 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +Mar-08 14:13:30.240 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +Mar-08 14:13:30.248 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY +Mar-08 14:13:30.248 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY +Mar-08 14:13:30.249 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY +Mar-08 14:13:30.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +Mar-08 14:13:30.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +Mar-08 14:13:30.263 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS +Mar-08 14:13:30.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS +Mar-08 14:13:30.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS +Mar-08 14:13:30.265 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +Mar-08 14:13:30.265 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +Mar-08 14:13:30.273 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED +Mar-08 14:13:30.274 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED +Mar-08 14:13:30.274 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED +Mar-08 14:13:30.274 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +Mar-08 14:13:30.275 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +Mar-08 14:13:30.290 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST +Mar-08 14:13:30.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_BEDTOINTERVALLIST` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST +Mar-08 14:13:30.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST +Mar-08 14:13:30.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST +Mar-08 14:13:30.294 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +Mar-08 14:13:30.294 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +Mar-08 14:13:30.302 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT +Mar-08 14:13:30.303 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF_TO_REFFLAT` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT +Mar-08 14:13:30.304 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT +Mar-08 14:13:30.304 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT +Mar-08 14:13:30.306 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +Mar-08 14:13:30.306 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +Mar-08 14:13:30.322 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: SAMTOOLS_VIEW_FOR_STARFUSION, SAMTOOLS_SORT_FOR_ARRIBA, GATK4_BEDTOINTERVALLIST, STAR_FOR_ARRIBA, STARFUSION_DOWNLOAD, FUSIONCATCHER, FUSIONCATCHER_DOWNLOAD, STAR_FOR_STARFUSION, GATK4_CREATESEQUENCEDICTIONARY, FASTP, FASTQC_FOR_FASTP, ENSEMBL_DOWNLOAD, GATK4_MARKDUPLICATES, CAT_FASTQ, GTF_TO_REFFLAT, STARFUSION, NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST, NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY, NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED, VCF_COLLECT, SAMTOOLS_INDEX_FOR_ARRIBA, ARRIBA_VISUALISATION, CONVERT2BED, FUSIONREPORT_DOWNLOAD, STAR_ALIGN, SAMTOOLS_INDEX_FOR_STARFUSION, FUSIONINSPECTOR, SAMTOOLS_INDEX, FASTQC, ARRIBA_DOWNLOAD, NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD, MULTIQC, NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD, STRINGTIE_MERGE, SAMTOOLS_SORT, SAMTOOLS_INDEX_FOR_STARFUSION_CRAM, SAMTOOLS_VIEW_FOR_ARRIBA, NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT, NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX, STARFUSION_BUILD, CAT_CAT, PICARD_COLLECTRNASEQMETRICS, HGNC_DOWNLOAD, SAMTOOLS_VIEW, SAMTOOLS_FAIDX, FUSIONREPORT, RRNA_TRANSCRIPTS, AGAT_CONVERTSPGFF2TSV, STRINGTIE_STRINGTIE, PICARD_COLLECTINSERTSIZEMETRICS, ARRIBA, NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS, STAR_GENOMEGENERATE +Mar-08 14:13:30.337 [main] WARN nextflow.Session - There's no process matching config selector: SAMPLESHEET_CHECK +Mar-08 14:13:30.337 [main] DEBUG nextflow.Session - Igniting dataflow network (25) +Mar-08 14:13:30.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD +Mar-08 14:13:30.370 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD +Mar-08 14:13:30.371 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX +Mar-08 14:13:30.371 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY +Mar-08 14:13:30.372 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS +Mar-08 14:13:30.372 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED +Mar-08 14:13:30.373 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST +Mar-08 14:13:30.373 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT +Mar-08 14:13:30.373 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination +Mar-08 14:13:30.373 [main] DEBUG nextflow.Session - Session await +Mar-08 14:13:30.553 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD] cache hash: 7f18070817f5b2ac14c8e745abfb6933; mode: STANDARD; entries: + 338337db5eff3bff24c213e2d8964e63 [java.util.UUID] 1bbe00d2-1928-4556-b97c-ecef4af4222e + 5dd471f5f4c9a54dea64867d4265ee28 [java.lang.String] NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD + 9ff7290eb13332bf5c4063dc712689d6 [java.lang.String] """ + wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt + date +%Y-%m-%d/%H:%M > HGNC-DB-timestamp.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml) + END_VERSIONS + """ + + 00c7c646a986ea5502fb404ea15e7443 [java.lang.String] quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5 + 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ + 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true + 77476d335f7c3b5b95495d42532f58d0 [java.util.HashMap$EntrySet] [task.process=NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD] + +Mar-08 14:13:30.613 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD] cache hash: dd31277bda420c7e0145fc89ea8613e5; mode: STANDARD; entries: + 338337db5eff3bff24c213e2d8964e63 [java.util.UUID] 1bbe00d2-1928-4556-b97c-ecef4af4222e + f65e11932b552ca585de284c5e5d0162 [java.lang.String] NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD + 0955cd72953c2b84dffe718d8e97dc15 [java.lang.String] """ + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.chromosome.{1..22}.fa.gz + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.chromosome.{MT,X,Y}.fa.gz + + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/cdna/Homo_sapiens.${params.genome}.cdna.all.fa.gz -O Homo_sapiens.${params.genome}.${ensembl_version}.cdna.all.fa.gz + + gunzip -c Homo_sapiens.${params.genome}.dna.chromosome.* > Homo_sapiens.${params.genome}.${ensembl_version}.all.fa + gunzip Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz + gunzip Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz + + + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml) + END_VERSIONS + """ + + 00c7c646a986ea5502fb404ea15e7443 [java.lang.String] quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5 + fee0e11be1152749b19f3d19542d3901 [java.lang.String] ensembl_version + f56f0c2893db292d86b93804fe80b6ac [java.lang.Integer] 102 + d9c152f5939e0f93a25dbd62b7c4d0a5 [java.lang.String] genome + 6b15613e5b490261f4ffe786a92c5825 [java.lang.String] GRCh38 + 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta + cb0f105a57d4145f7acb92ca9cf2ea12 [java.util.LinkedHashMap] [id:Homo_sapiens.GRCh38.102] + 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ + 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true + c877f2c88b6ad8c3dbe3236a80f57755 [java.util.HashMap$EntrySet] [task.process=NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD, params.genome=GRCh38] + +Mar-08 14:13:30.754 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run +Mar-08 14:13:30.756 [Task submitter] INFO nextflow.Session - [81/2c2c1f] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) +Mar-08 14:13:30.864 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run +Mar-08 14:13:30.865 [Task submitter] INFO nextflow.Session - [52/33e328] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl) +Mar-08 14:14:06.817 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc); status: COMPLETED; exit: 0; error: -; workDir: /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work/81/2c2c1f77cfe71f861687ce1e2e35ba] +Mar-08 14:14:06.983 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false +Mar-08 14:14:10.653 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT +Mar-08 14:14:10.717 [SIGINT handler] DEBUG nextflow.Session - The following nodes are still active: +[process] NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX + status=ACTIVE + port 0: (value) OPEN ; channel: - + port 1: (value) bound ; channel: - + port 2: (cntrl) - ; channel: $ + +[process] NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY + status=ACTIVE + port 0: (value) OPEN ; channel: - + port 1: (cntrl) - ; channel: $ + +[process] NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS + status=ACTIVE + port 0: (value) OPEN ; channel: - + port 1: (cntrl) - ; channel: $ + +[process] NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED + status=ACTIVE + port 0: (value) OPEN ; channel: - + port 1: (cntrl) - ; channel: $ + +[process] NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST + status=ACTIVE + port 0: (value) OPEN ; channel: - + port 1: (value) OPEN ; channel: - + port 2: (cntrl) - ; channel: $ + +[process] NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT + status=ACTIVE + port 0: (value) OPEN ; channel: - + port 1: (cntrl) - ; channel: $ + +Mar-08 14:14:10.812 [main] DEBUG nextflow.Session - Session await > all processes finished +Mar-08 14:14:10.813 [main] DEBUG nextflow.Session - Session await > all barriers passed +Mar-08 14:14:10.829 [main] INFO nextflow.Nextflow - -[nf-core/rnafusion] Pipeline completed with errors- +Mar-08 14:14:10.840 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (1) +Mar-08 14:14:10.874 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=1; retriesCount=0; abortedCount=0; succeedDuration=52s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=4; peakMemory=6 GB; ] +Mar-08 14:14:10.875 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file +Mar-08 14:14:10.897 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done +Mar-08 14:14:10.897 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-validation@1.1.3' +Mar-08 14:14:10.898 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation +Mar-08 14:14:11.002 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json new file mode 100644 index 00000000..eda4f800 --- /dev/null +++ b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json @@ -0,0 +1 @@ +{"input":"https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv","cosmic_username":null,"build_references":true,"genome_base":"references","cosmic_passwd":null,"max_time":"6.h","max_cpus":2,"max_memory":"6.GB","outdir":"results"} \ No newline at end of file diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.err b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.err new file mode 100644 index 00000000..e69de29b diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.out b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.out new file mode 100644 index 00000000..7b566f86 --- /dev/null +++ b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.out @@ -0,0 +1,145 @@ +N E X T F L O W ~ version 23.04.1 +Launching `/Users/annick.renevey/Projects/rnafusion/tests/../main.nf` [cheesy_hawking] DSL2 - revision: 12cef51b71 +WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` + + +------------------------------------------------------ + ,--./,-. + ___ __ __ __ ___ /,-._.--~' + |\ | |__ __ / ` / \ |__) |__ } { + | \| | \__, \__/ | \ |___ \`-._,-`-, + `._,._,' + nf-core/rnafusion v3.0.2dev +------------------------------------------------------ +Core Nextflow options + runName : cheesy_hawking + containerEngine : docker + launchDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997 + workDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work + projectDir : /Users/annick.renevey/Projects/rnafusion + userName : annick.renevey + profile : debug,test,docker + configFiles :  + +Input/output options + input : https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv + outdir : results + build_references : true + genomes_base : results/references + starfusion_build : true + arriba_ref : results/references/arriba + arriba_ref_blacklist : results/references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz + arriba_ref_cytobands : results/references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv + arriba_ref_known_fusions : results/references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz + arriba_ref_protein_domains : results/references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3 + ensembl_ref : results/references/ensembl + fusioncatcher_limitSjdbInsertNsj : 2000000 + fusioncatcher_ref : results/references/fusioncatcher/human_v102 + fusioninspector_limitSjdbInsertNsj: 1000000 + fusionreport_ref : results/references/fusion_report_db + hgnc_ref : results/references/hgnc/hgnc_complete_set.txt + hgnc_date : results/references/hgnc/HGNC-DB-timestamp.txt + starfusion_ref : results/references/starfusion/ctat_genome_lib_build_dir + starindex_ref : results/references/star + tools_cutoff : 1 + +Read trimming options + adapter_fasta : [] + +Alignment compression options + cram : [] + +Reference genome options + genome : GRCh38 + fasta : results/references/ensembl/Homo_sapiens.GRCh38.102.all.fa + fai : results/references/ensembl/Homo_sapiens.GRCh38.102.all.fa.fai + gtf : results/references/ensembl/Homo_sapiens.GRCh38.102.gtf + chrgtf : results/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf + transcript : results/references/ensembl/Homo_sapiens.GRCh38.102.cdna.all.fa.gz + refflat : results/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf.refflat + rrna_intervals : results/references/ensembl/Homo_sapiens.GRCh38.102.interval_list + +Institutional config options + config_profile_name : Test profile + config_profile_description : Minimal test dataset to check pipeline function + +Max job request options + max_cpus : 2 + max_memory : 6.GB + max_time : 6.h + +!! Only displaying parameters that differ from the pipeline defaults !! +------------------------------------------------------ +If you use nf-core/rnafusion for your analysis please cite: + +* The pipeline + + +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x + +* Software dependencies + https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md +------------------------------------------------------ +WARN: The following invalid input values have been detected: + +* --genome_base: references +* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/ +* --pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/ + + +WARN: There's no process matching config selector: SAMPLESHEET_CHECK +[NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD] cache hash: 7f18070817f5b2ac14c8e745abfb6933; mode: STANDARD; entries: + 338337db5eff3bff24c213e2d8964e63 [java.util.UUID] 1bbe00d2-1928-4556-b97c-ecef4af4222e + 5dd471f5f4c9a54dea64867d4265ee28 [java.lang.String] NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD + 9ff7290eb13332bf5c4063dc712689d6 [java.lang.String] """ + wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt + date +%Y-%m-%d/%H:%M > HGNC-DB-timestamp.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml) + END_VERSIONS + """ + + 00c7c646a986ea5502fb404ea15e7443 [java.lang.String] quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5 + 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ + 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true + 77476d335f7c3b5b95495d42532f58d0 [java.util.HashMap$EntrySet] [task.process=NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD] + +[NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD] cache hash: dd31277bda420c7e0145fc89ea8613e5; mode: STANDARD; entries: + 338337db5eff3bff24c213e2d8964e63 [java.util.UUID] 1bbe00d2-1928-4556-b97c-ecef4af4222e + f65e11932b552ca585de284c5e5d0162 [java.lang.String] NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD + 0955cd72953c2b84dffe718d8e97dc15 [java.lang.String] """ + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.chromosome.{1..22}.fa.gz + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.chromosome.{MT,X,Y}.fa.gz + + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz + wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/cdna/Homo_sapiens.${params.genome}.cdna.all.fa.gz -O Homo_sapiens.${params.genome}.${ensembl_version}.cdna.all.fa.gz + + gunzip -c Homo_sapiens.${params.genome}.dna.chromosome.* > Homo_sapiens.${params.genome}.${ensembl_version}.all.fa + gunzip Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz + gunzip Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz + + + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml) + END_VERSIONS + """ + + 00c7c646a986ea5502fb404ea15e7443 [java.lang.String] quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5 + fee0e11be1152749b19f3d19542d3901 [java.lang.String] ensembl_version + f56f0c2893db292d86b93804fe80b6ac [java.lang.Integer] 102 + d9c152f5939e0f93a25dbd62b7c4d0a5 [java.lang.String] genome + 6b15613e5b490261f4ffe786a92c5825 [java.lang.String] GRCh38 + 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta + cb0f105a57d4145f7acb92ca9cf2ea12 [java.util.LinkedHashMap] [id:Homo_sapiens.GRCh38.102] + 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ + 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true + c877f2c88b6ad8c3dbe3236a80f57755 [java.util.HashMap$EntrySet] [task.process=NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD, params.genome=GRCh38] + +[81/2c2c1f] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) +[52/33e328] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl) diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv new file mode 100644 index 00000000..57aed492 --- /dev/null +++ b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv @@ -0,0 +1,3 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar +1 81/2c2c1f 89776 NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) COMPLETED 0 2024-03-08 14:13:30.756 36s 26s 3.0% 24.8 MB 2.3 GB 16.2 MB 15.8 MB +2 52/33e328 89787 NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl) ABORTED - 2024-03-08 14:13:30.864 - - - - - - - From 27ae59d1f6e51cad4041858dcc97c76b04fc7e0e Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Mar 2024 15:08:43 +0100 Subject: [PATCH 21/28] prettier --- .../meta/params.json | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json index eda4f800..691664e7 100644 --- a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json +++ b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json @@ -1 +1,11 @@ -{"input":"https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv","cosmic_username":null,"build_references":true,"genome_base":"references","cosmic_passwd":null,"max_time":"6.h","max_cpus":2,"max_memory":"6.GB","outdir":"results"} \ No newline at end of file +{ + "input": "https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv", + "cosmic_username": null, + "build_references": true, + "genome_base": "references", + "cosmic_passwd": null, + "max_time": "6.h", + "max_cpus": 2, + "max_memory": "6.GB", + "outdir": "results" +} From c4fb47d53b67ae5aeb1d5e25e06e554e5c5706c0 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Mar 2024 15:10:52 +0100 Subject: [PATCH 22/28] remove tests --- .../meta/assets | 1 - .../818076bdee20d7e7df39ccd4d6617997/meta/bin | 1 - .../meta/nextflow.log | 314 ------------------ .../meta/params.json | 11 - .../meta/std.err | 0 .../meta/std.out | 145 -------- .../meta/trace.csv | 3 - 7 files changed, 475 deletions(-) delete mode 120000 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/assets delete mode 120000 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/bin delete mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log delete mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json delete mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.err delete mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.out delete mode 100644 .nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/assets b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/assets deleted file mode 120000 index e4ea7900..00000000 --- a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/assets +++ /dev/null @@ -1 +0,0 @@ -/Users/annick.renevey/Projects/rnafusion/assets \ No newline at end of file diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/bin b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/bin deleted file mode 120000 index db857c9f..00000000 --- a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/bin +++ /dev/null @@ -1 +0,0 @@ -/Users/annick.renevey/Projects/rnafusion/bin \ No newline at end of file diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log deleted file mode 100644 index 586050f1..00000000 --- a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log +++ /dev/null @@ -1,314 +0,0 @@ -Mar-08 14:13:11.080 [main] DEBUG nextflow.cli.Launcher - $> nextflow -log /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/nextflow.log run /Users/annick.renevey/Projects/rnafusion/tests/../main.nf -c /Users/annick.renevey/Projects/rnafusion/nextflow.config -c /Users/annick.renevey/Projects/rnafusion/tests/nextflow.config -params-file /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json -ansi-log false -profile debug,test,docker -with-trace /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv -w /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work -Mar-08 14:13:11.190 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.1 -Mar-08 14:13:11.228 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/Users/annick.renevey/.nextflow/plugins; core-plugins: nf-amazon@1.16.2,nf-azure@1.0.1,nf-codecommit@0.1.4,nf-console@1.0.5,nf-ga4gh@1.0.5,nf-google@1.7.3,nf-tower@1.5.12,nf-wave@0.8.2 -Mar-08 14:13:11.245 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] -Mar-08 14:13:11.246 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] -Mar-08 14:13:11.250 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode -Mar-08 14:13:11.269 [main] INFO org.pf4j.AbstractPluginManager - No plugins -Mar-08 14:13:11.303 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /Users/annick.renevey/Projects/rnafusion/nextflow.config -Mar-08 14:13:11.310 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/rnafusion/nextflow.config -Mar-08 14:13:11.311 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /Users/annick.renevey/Projects/rnafusion/tests/nextflow.config -Mar-08 14:13:11.311 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/rnafusion/nextflow.config -Mar-08 14:13:11.311 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/rnafusion/nextflow.config -Mar-08 14:13:11.311 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /Users/annick.renevey/Projects/rnafusion/tests/nextflow.config -Mar-08 14:13:11.393 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `debug,test,docker` -Mar-08 14:13:16.099 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `debug,test,docker` -Mar-08 14:13:17.277 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `debug,test,docker` -Mar-08 14:13:17.413 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, imperial, maestro, software_license, utd_europa, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, ethz_euler, test_full, imb, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] -Mar-08 14:13:17.512 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion -Mar-08 14:13:17.534 [main] INFO nextflow.cli.CmdRun - Launching `/Users/annick.renevey/Projects/rnafusion/tests/../main.nf` [cheesy_hawking] DSL2 - revision: 12cef51b71 -Mar-08 14:13:17.536 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation@1.1.3] -Mar-08 14:13:17.541 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] -Mar-08 14:13:17.541 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation@1.1.3] -Mar-08 14:13:17.542 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3 -Mar-08 14:13:17.559 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved -Mar-08 14:13:17.560 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3' -Mar-08 14:13:17.592 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3 -Mar-08 14:13:17.616 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /Users/annick.renevey/.nextflow/secrets/store.json -Mar-08 14:13:17.628 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@57e03347] - activable => nextflow.secret.LocalSecretsProvider@57e03347 -Mar-08 14:13:17.713 [main] DEBUG nextflow.Session - Session UUID: 1bbe00d2-1928-4556-b97c-ecef4af4222e -Mar-08 14:13:17.713 [main] DEBUG nextflow.Session - Run name: cheesy_hawking -Mar-08 14:13:17.714 [main] DEBUG nextflow.Session - Executor pool size: 8 -Mar-08 14:13:17.727 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false -Mar-08 14:13:17.787 [main] DEBUG nextflow.cli.CmdRun - - Version: 23.04.1 build 5866 - Created: 15-04-2023 06:51 UTC (08:51 CEST) - System: Mac OS X 14.2.1 - Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.3+7-LTS - Encoding: UTF-8 (UTF-8) - Process: 89543@annickrmbp [130.229.140.244] - CPUs: 8 - Mem: 16 GB (22.8 MB) - Swap: 6 GB (1.4 GB) -Mar-08 14:13:17.818 [main] DEBUG nextflow.Session - Work-dir: /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work [Mac OS X] -Mar-08 14:13:17.840 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] -Mar-08 14:13:17.857 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory -Mar-08 14:13:17.959 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory -Mar-08 14:13:17.990 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000 -Mar-08 14:13:18.140 [main] DEBUG nextflow.Session - Session start -Mar-08 14:13:18.175 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv -Mar-08 14:13:18.579 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution -Mar-08 14:13:19.365 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation -Mar-08 14:13:19.385 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation -Mar-08 14:13:19.385 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation -Mar-08 14:13:19.411 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation -Mar-08 14:13:19.413 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation -Mar-08 14:13:22.583 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation -Mar-08 14:13:22.586 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation -Mar-08 14:13:22.586 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation -Mar-08 14:13:22.588 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation -Mar-08 14:13:22.588 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation -Mar-08 14:13:22.738 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation -Mar-08 14:13:27.381 [main] DEBUG nextflow.Nextflow - Using schema file: nextflow_schema.json -Mar-08 14:13:27.389 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` -Mar-08 14:13:27.418 [main] INFO nextflow.Nextflow - - ------------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~' - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' - nf-core/rnafusion v3.0.2dev ------------------------------------------------------- -Core Nextflow options - runName : cheesy_hawking - containerEngine : docker - launchDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997 - workDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work - projectDir : /Users/annick.renevey/Projects/rnafusion - userName : annick.renevey - profile : debug,test,docker - configFiles :  - -Input/output options - input : https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv - outdir : results - build_references : true - genomes_base : results/references - starfusion_build : true - arriba_ref : results/references/arriba - arriba_ref_blacklist : results/references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz - arriba_ref_cytobands : results/references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv - arriba_ref_known_fusions : results/references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz - arriba_ref_protein_domains : results/references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3 - ensembl_ref : results/references/ensembl - fusioncatcher_limitSjdbInsertNsj : 2000000 - fusioncatcher_ref : results/references/fusioncatcher/human_v102 - fusioninspector_limitSjdbInsertNsj: 1000000 - fusionreport_ref : results/references/fusion_report_db - hgnc_ref : results/references/hgnc/hgnc_complete_set.txt - hgnc_date : results/references/hgnc/HGNC-DB-timestamp.txt - starfusion_ref : results/references/starfusion/ctat_genome_lib_build_dir - starindex_ref : results/references/star - tools_cutoff : 1 - -Read trimming options - adapter_fasta : [] - -Alignment compression options - cram : [] - -Reference genome options - genome : GRCh38 - fasta : results/references/ensembl/Homo_sapiens.GRCh38.102.all.fa - fai : results/references/ensembl/Homo_sapiens.GRCh38.102.all.fa.fai - gtf : results/references/ensembl/Homo_sapiens.GRCh38.102.gtf - chrgtf : results/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf - transcript : results/references/ensembl/Homo_sapiens.GRCh38.102.cdna.all.fa.gz - refflat : results/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf.refflat - rrna_intervals : results/references/ensembl/Homo_sapiens.GRCh38.102.interval_list - -Institutional config options - config_profile_name : Test profile - config_profile_description : Minimal test dataset to check pipeline function - -Max job request options - max_cpus : 2 - max_memory : 6.GB - max_time : 6.h - -!! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------- -If you use nf-core/rnafusion for your analysis please cite: - -* The pipeline - - -* The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies - https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md ------------------------------------------------------- -Mar-08 14:13:27.425 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation -Mar-08 14:13:27.617 [main] WARN nextflow.validation.SchemaValidator - The following invalid input values have been detected: - -* --genome_base: references -* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/ -* --pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/ - - -Mar-08 14:13:27.912 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' with '/Users/annick.renevey/Projects/rnafusion/assets/schema_input.json' -Mar-08 14:13:29.935 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv' with '/Users/annick.renevey/Projects/rnafusion/assets/schema_input.json' -Mar-08 14:13:29.935 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation -Mar-08 14:13:30.046 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD -Mar-08 14:13:30.049 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:ENSEMBL_DOWNLOAD` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD -Mar-08 14:13:30.050 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD -Mar-08 14:13:30.053 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD -Mar-08 14:13:30.061 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -Mar-08 14:13:30.061 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -Mar-08 14:13:30.083 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local -Mar-08 14:13:30.090 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=16 GB; capacity=8; pollInterval=100ms; dumpInterval=5m -Mar-08 14:13:30.203 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD -Mar-08 14:13:30.204 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:HGNC_DOWNLOAD` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD -Mar-08 14:13:30.206 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD -Mar-08 14:13:30.207 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD -Mar-08 14:13:30.213 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -Mar-08 14:13:30.214 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -Mar-08 14:13:30.236 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX -Mar-08 14:13:30.237 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX -Mar-08 14:13:30.238 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX -Mar-08 14:13:30.238 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX -Mar-08 14:13:30.240 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -Mar-08 14:13:30.240 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -Mar-08 14:13:30.248 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY -Mar-08 14:13:30.248 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY -Mar-08 14:13:30.249 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY -Mar-08 14:13:30.250 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -Mar-08 14:13:30.250 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -Mar-08 14:13:30.263 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS -Mar-08 14:13:30.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS -Mar-08 14:13:30.264 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS -Mar-08 14:13:30.265 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -Mar-08 14:13:30.265 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -Mar-08 14:13:30.273 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED -Mar-08 14:13:30.274 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED -Mar-08 14:13:30.274 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED -Mar-08 14:13:30.274 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -Mar-08 14:13:30.275 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -Mar-08 14:13:30.290 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST -Mar-08 14:13:30.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GATK4_BEDTOINTERVALLIST` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST -Mar-08 14:13:30.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST -Mar-08 14:13:30.292 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST -Mar-08 14:13:30.294 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -Mar-08 14:13:30.294 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -Mar-08 14:13:30.302 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT -Mar-08 14:13:30.303 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF_TO_REFFLAT` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT -Mar-08 14:13:30.304 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT -Mar-08 14:13:30.304 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:.*` matches process NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT -Mar-08 14:13:30.306 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -Mar-08 14:13:30.306 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -Mar-08 14:13:30.322 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: SAMTOOLS_VIEW_FOR_STARFUSION, SAMTOOLS_SORT_FOR_ARRIBA, GATK4_BEDTOINTERVALLIST, STAR_FOR_ARRIBA, STARFUSION_DOWNLOAD, FUSIONCATCHER, FUSIONCATCHER_DOWNLOAD, STAR_FOR_STARFUSION, GATK4_CREATESEQUENCEDICTIONARY, FASTP, FASTQC_FOR_FASTP, ENSEMBL_DOWNLOAD, GATK4_MARKDUPLICATES, CAT_FASTQ, GTF_TO_REFFLAT, STARFUSION, NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST, NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY, NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED, VCF_COLLECT, SAMTOOLS_INDEX_FOR_ARRIBA, ARRIBA_VISUALISATION, CONVERT2BED, FUSIONREPORT_DOWNLOAD, STAR_ALIGN, SAMTOOLS_INDEX_FOR_STARFUSION, FUSIONINSPECTOR, SAMTOOLS_INDEX, FASTQC, ARRIBA_DOWNLOAD, NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD, MULTIQC, NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD, STRINGTIE_MERGE, SAMTOOLS_SORT, SAMTOOLS_INDEX_FOR_STARFUSION_CRAM, SAMTOOLS_VIEW_FOR_ARRIBA, NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT, NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX, STARFUSION_BUILD, CAT_CAT, PICARD_COLLECTRNASEQMETRICS, HGNC_DOWNLOAD, SAMTOOLS_VIEW, SAMTOOLS_FAIDX, FUSIONREPORT, RRNA_TRANSCRIPTS, AGAT_CONVERTSPGFF2TSV, STRINGTIE_STRINGTIE, PICARD_COLLECTINSERTSIZEMETRICS, ARRIBA, NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS, STAR_GENOMEGENERATE -Mar-08 14:13:30.337 [main] WARN nextflow.Session - There's no process matching config selector: SAMPLESHEET_CHECK -Mar-08 14:13:30.337 [main] DEBUG nextflow.Session - Igniting dataflow network (25) -Mar-08 14:13:30.369 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD -Mar-08 14:13:30.370 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD -Mar-08 14:13:30.371 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX -Mar-08 14:13:30.371 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY -Mar-08 14:13:30.372 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS -Mar-08 14:13:30.372 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED -Mar-08 14:13:30.373 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST -Mar-08 14:13:30.373 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT -Mar-08 14:13:30.373 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination -Mar-08 14:13:30.373 [main] DEBUG nextflow.Session - Session await -Mar-08 14:13:30.553 [Actor Thread 17] INFO nextflow.processor.TaskProcessor - [NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD] cache hash: 7f18070817f5b2ac14c8e745abfb6933; mode: STANDARD; entries: - 338337db5eff3bff24c213e2d8964e63 [java.util.UUID] 1bbe00d2-1928-4556-b97c-ecef4af4222e - 5dd471f5f4c9a54dea64867d4265ee28 [java.lang.String] NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD - 9ff7290eb13332bf5c4063dc712689d6 [java.lang.String] """ - wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt - date +%Y-%m-%d/%H:%M > HGNC-DB-timestamp.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml) - END_VERSIONS - """ - - 00c7c646a986ea5502fb404ea15e7443 [java.lang.String] quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5 - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - 77476d335f7c3b5b95495d42532f58d0 [java.util.HashMap$EntrySet] [task.process=NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD] - -Mar-08 14:13:30.613 [Actor Thread 15] INFO nextflow.processor.TaskProcessor - [NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD] cache hash: dd31277bda420c7e0145fc89ea8613e5; mode: STANDARD; entries: - 338337db5eff3bff24c213e2d8964e63 [java.util.UUID] 1bbe00d2-1928-4556-b97c-ecef4af4222e - f65e11932b552ca585de284c5e5d0162 [java.lang.String] NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD - 0955cd72953c2b84dffe718d8e97dc15 [java.lang.String] """ - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.chromosome.{1..22}.fa.gz - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.chromosome.{MT,X,Y}.fa.gz - - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/cdna/Homo_sapiens.${params.genome}.cdna.all.fa.gz -O Homo_sapiens.${params.genome}.${ensembl_version}.cdna.all.fa.gz - - gunzip -c Homo_sapiens.${params.genome}.dna.chromosome.* > Homo_sapiens.${params.genome}.${ensembl_version}.all.fa - gunzip Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz - gunzip Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz - - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml) - END_VERSIONS - """ - - 00c7c646a986ea5502fb404ea15e7443 [java.lang.String] quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5 - fee0e11be1152749b19f3d19542d3901 [java.lang.String] ensembl_version - f56f0c2893db292d86b93804fe80b6ac [java.lang.Integer] 102 - d9c152f5939e0f93a25dbd62b7c4d0a5 [java.lang.String] genome - 6b15613e5b490261f4ffe786a92c5825 [java.lang.String] GRCh38 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cb0f105a57d4145f7acb92ca9cf2ea12 [java.util.LinkedHashMap] [id:Homo_sapiens.GRCh38.102] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - c877f2c88b6ad8c3dbe3236a80f57755 [java.util.HashMap$EntrySet] [task.process=NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD, params.genome=GRCh38] - -Mar-08 14:13:30.754 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run -Mar-08 14:13:30.756 [Task submitter] INFO nextflow.Session - [81/2c2c1f] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) -Mar-08 14:13:30.864 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run -Mar-08 14:13:30.865 [Task submitter] INFO nextflow.Session - [52/33e328] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl) -Mar-08 14:14:06.817 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc); status: COMPLETED; exit: 0; error: -; workDir: /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work/81/2c2c1f77cfe71f861687ce1e2e35ba] -Mar-08 14:14:06.983 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false -Mar-08 14:14:10.653 [SIGINT handler] DEBUG nextflow.Session - Session aborted -- Cause: SIGINT -Mar-08 14:14:10.717 [SIGINT handler] DEBUG nextflow.Session - The following nodes are still active: -[process] NFCORE_RNAFUSION:BUILD_REFERENCES:SAMTOOLS_FAIDX - status=ACTIVE - port 0: (value) OPEN ; channel: - - port 1: (value) bound ; channel: - - port 2: (cntrl) - ; channel: $ - -[process] NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_CREATESEQUENCEDICTIONARY - status=ACTIVE - port 0: (value) OPEN ; channel: - - port 1: (cntrl) - ; channel: $ - -[process] NFCORE_RNAFUSION:BUILD_REFERENCES:RRNA_TRANSCRIPTS - status=ACTIVE - port 0: (value) OPEN ; channel: - - port 1: (cntrl) - ; channel: $ - -[process] NFCORE_RNAFUSION:BUILD_REFERENCES:CONVERT2BED - status=ACTIVE - port 0: (value) OPEN ; channel: - - port 1: (cntrl) - ; channel: $ - -[process] NFCORE_RNAFUSION:BUILD_REFERENCES:GATK4_BEDTOINTERVALLIST - status=ACTIVE - port 0: (value) OPEN ; channel: - - port 1: (value) OPEN ; channel: - - port 2: (cntrl) - ; channel: $ - -[process] NFCORE_RNAFUSION:BUILD_REFERENCES:GTF_TO_REFFLAT - status=ACTIVE - port 0: (value) OPEN ; channel: - - port 1: (cntrl) - ; channel: $ - -Mar-08 14:14:10.812 [main] DEBUG nextflow.Session - Session await > all processes finished -Mar-08 14:14:10.813 [main] DEBUG nextflow.Session - Session await > all barriers passed -Mar-08 14:14:10.829 [main] INFO nextflow.Nextflow - -[nf-core/rnafusion] Pipeline completed with errors- -Mar-08 14:14:10.840 [main] WARN n.processor.TaskPollingMonitor - Killing running tasks (1) -Mar-08 14:14:10.874 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=1; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=1; retriesCount=0; abortedCount=0; succeedDuration=52s; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=2; peakCpus=4; peakMemory=6 GB; ] -Mar-08 14:14:10.875 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file -Mar-08 14:14:10.897 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done -Mar-08 14:14:10.897 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-validation@1.1.3' -Mar-08 14:14:10.898 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation -Mar-08 14:14:11.002 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json deleted file mode 100644 index 691664e7..00000000 --- a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/params.json +++ /dev/null @@ -1,11 +0,0 @@ -{ - "input": "https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv", - "cosmic_username": null, - "build_references": true, - "genome_base": "references", - "cosmic_passwd": null, - "max_time": "6.h", - "max_cpus": 2, - "max_memory": "6.GB", - "outdir": "results" -} diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.err b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.err deleted file mode 100644 index e69de29b..00000000 diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.out b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.out deleted file mode 100644 index 7b566f86..00000000 --- a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/std.out +++ /dev/null @@ -1,145 +0,0 @@ -N E X T F L O W ~ version 23.04.1 -Launching `/Users/annick.renevey/Projects/rnafusion/tests/../main.nf` [cheesy_hawking] DSL2 - revision: 12cef51b71 -WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value` - - ------------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~' - |\ | |__ __ / ` / \ |__) |__ } { - | \| | \__, \__/ | \ |___ \`-._,-`-, - `._,._,' - nf-core/rnafusion v3.0.2dev ------------------------------------------------------- -Core Nextflow options - runName : cheesy_hawking - containerEngine : docker - launchDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997 - workDir : /Users/annick.renevey/Projects/rnafusion/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/work - projectDir : /Users/annick.renevey/Projects/rnafusion - userName : annick.renevey - profile : debug,test,docker - configFiles :  - -Input/output options - input : https://raw.githubusercontent.com/nf-core/test-datasets/rnafusion/testdata/human/samplesheet_valid.csv - outdir : results - build_references : true - genomes_base : results/references - starfusion_build : true - arriba_ref : results/references/arriba - arriba_ref_blacklist : results/references/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz - arriba_ref_cytobands : results/references/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv - arriba_ref_known_fusions : results/references/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz - arriba_ref_protein_domains : results/references/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3 - ensembl_ref : results/references/ensembl - fusioncatcher_limitSjdbInsertNsj : 2000000 - fusioncatcher_ref : results/references/fusioncatcher/human_v102 - fusioninspector_limitSjdbInsertNsj: 1000000 - fusionreport_ref : results/references/fusion_report_db - hgnc_ref : results/references/hgnc/hgnc_complete_set.txt - hgnc_date : results/references/hgnc/HGNC-DB-timestamp.txt - starfusion_ref : results/references/starfusion/ctat_genome_lib_build_dir - starindex_ref : results/references/star - tools_cutoff : 1 - -Read trimming options - adapter_fasta : [] - -Alignment compression options - cram : [] - -Reference genome options - genome : GRCh38 - fasta : results/references/ensembl/Homo_sapiens.GRCh38.102.all.fa - fai : results/references/ensembl/Homo_sapiens.GRCh38.102.all.fa.fai - gtf : results/references/ensembl/Homo_sapiens.GRCh38.102.gtf - chrgtf : results/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf - transcript : results/references/ensembl/Homo_sapiens.GRCh38.102.cdna.all.fa.gz - refflat : results/references/ensembl/Homo_sapiens.GRCh38.102.chr.gtf.refflat - rrna_intervals : results/references/ensembl/Homo_sapiens.GRCh38.102.interval_list - -Institutional config options - config_profile_name : Test profile - config_profile_description : Minimal test dataset to check pipeline function - -Max job request options - max_cpus : 2 - max_memory : 6.GB - max_time : 6.h - -!! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------- -If you use nf-core/rnafusion for your analysis please cite: - -* The pipeline - - -* The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies - https://github.com/nf-core/rnafusion/blob/master/CITATIONS.md ------------------------------------------------------- -WARN: The following invalid input values have been detected: - -* --genome_base: references -* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/ -* --pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/ - - -WARN: There's no process matching config selector: SAMPLESHEET_CHECK -[NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD] cache hash: 7f18070817f5b2ac14c8e745abfb6933; mode: STANDARD; entries: - 338337db5eff3bff24c213e2d8964e63 [java.util.UUID] 1bbe00d2-1928-4556-b97c-ecef4af4222e - 5dd471f5f4c9a54dea64867d4265ee28 [java.lang.String] NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD - 9ff7290eb13332bf5c4063dc712689d6 [java.lang.String] """ - wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt - date +%Y-%m-%d/%H:%M > HGNC-DB-timestamp.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml) - END_VERSIONS - """ - - 00c7c646a986ea5502fb404ea15e7443 [java.lang.String] quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5 - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - 77476d335f7c3b5b95495d42532f58d0 [java.util.HashMap$EntrySet] [task.process=NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD] - -[NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD] cache hash: dd31277bda420c7e0145fc89ea8613e5; mode: STANDARD; entries: - 338337db5eff3bff24c213e2d8964e63 [java.util.UUID] 1bbe00d2-1928-4556-b97c-ecef4af4222e - f65e11932b552ca585de284c5e5d0162 [java.lang.String] NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD - 0955cd72953c2b84dffe718d8e97dc15 [java.lang.String] """ - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.chromosome.{1..22}.fa.gz - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/dna/Homo_sapiens.${params.genome}.dna.chromosome.{MT,X,Y}.fa.gz - - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/gtf/homo_sapiens/Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz - wget ftp://ftp.ensembl.org/pub/release-${ensembl_version}/fasta/homo_sapiens/cdna/Homo_sapiens.${params.genome}.cdna.all.fa.gz -O Homo_sapiens.${params.genome}.${ensembl_version}.cdna.all.fa.gz - - gunzip -c Homo_sapiens.${params.genome}.dna.chromosome.* > Homo_sapiens.${params.genome}.${ensembl_version}.all.fa - gunzip Homo_sapiens.${params.genome}.${ensembl_version}.gtf.gz - gunzip Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf.gz - - - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml) - END_VERSIONS - """ - - 00c7c646a986ea5502fb404ea15e7443 [java.lang.String] quay.io/biocontainers/gnu-wget:1.18--h5bf99c6_5 - fee0e11be1152749b19f3d19542d3901 [java.lang.String] ensembl_version - f56f0c2893db292d86b93804fe80b6ac [java.lang.Integer] 102 - d9c152f5939e0f93a25dbd62b7c4d0a5 [java.lang.String] genome - 6b15613e5b490261f4ffe786a92c5825 [java.lang.String] GRCh38 - 22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta - cb0f105a57d4145f7acb92ca9cf2ea12 [java.util.LinkedHashMap] [id:Homo_sapiens.GRCh38.102] - 4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ - 16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true - c877f2c88b6ad8c3dbe3236a80f57755 [java.util.HashMap$EntrySet] [task.process=NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD, params.genome=GRCh38] - -[81/2c2c1f] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) -[52/33e328] Submitted process > NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl) diff --git a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv b/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv deleted file mode 100644 index 57aed492..00000000 --- a/.nf-test/tests/818076bdee20d7e7df39ccd4d6617997/meta/trace.csv +++ /dev/null @@ -1,3 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar -1 81/2c2c1f 89776 NFCORE_RNAFUSION:BUILD_REFERENCES:HGNC_DOWNLOAD (hgnc) COMPLETED 0 2024-03-08 14:13:30.756 36s 26s 3.0% 24.8 MB 2.3 GB 16.2 MB 15.8 MB -2 52/33e328 89787 NFCORE_RNAFUSION:BUILD_REFERENCES:ENSEMBL_DOWNLOAD (ensembl) ABORTED - 2024-03-08 14:13:30.864 - - - - - - - From 9313a47e5c62830c66d580589098b87cad2d54e9 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 15 Mar 2024 15:33:33 +0200 Subject: [PATCH 23/28] fix ci --- main.nf | 13 ++++++++++++- workflows/rnafusion.nf | 7 ++++++- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 8ba6f049..ac96ab66 100644 --- a/main.nf +++ b/main.nf @@ -24,6 +24,16 @@ include { BUILD_REFERENCES } from './workflows/build_references' include { RNAFUSION } from './workflows/rnafusion' +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + GENOME PARAMETER VALUES +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + + + + + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -43,7 +53,8 @@ workflow NFCORE_RNAFUSION { if (params.build_references) { BUILD_REFERENCES () } else { - RNAFUSION() + ch_samplesheet = Channel.value(file(params.input, checkIfExists: true)) + RNAFUSION(ch_samplesheet) } } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index a1b8f431..511b121b 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -68,6 +68,11 @@ include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' workflow RNAFUSION { + take: + ch_samplesheet + + main: + ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() @@ -77,7 +82,7 @@ workflow RNAFUSION { Channel .fromSamplesheet("input") .map { - meta, fastq_1, fastq_2 -> + meta, fastq_1, fastq_2, strandedness -> if (!fastq_2) { return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] } else { From 1ea6a3aff55d067a17097f3a2bdd7a6847c9a6e1 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 15 Mar 2024 16:29:10 +0200 Subject: [PATCH 24/28] add // --- .../utils_nfcore_rnafusion_pipeline/main.nf | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf index e7d4e72d..3a02b058 100644 --- a/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf @@ -233,3 +233,26 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + +// +// Function to generate an error if contigs in genome fasta file > 512 Mbp +// +def checkMaxContigSize(fai_file) { + def max_size = 512000000 + fai_file.eachLine { line -> + def lspl = line.split('\t') + def chrom = lspl[0] + def size = lspl[1] + if (size.toInteger() > max_size) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Contig longer than ${max_size}bp found in reference genome!\n\n" + + " ${chrom}: ${size}\n\n" + + " Provide the '--bam_csi_index' parameter to use a CSI instead of BAI index.\n\n" + + " Please see:\n" + + " https://github.com/nf-core/rnaseq/issues/744\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } + } +} + From 6e2408689ab6d5f1c9a605d284ae0c20e6e87cf7 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 15 Mar 2024 16:29:23 +0200 Subject: [PATCH 25/28] checkMaxContigSize function --- 512 | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 512 diff --git a/512 b/512 new file mode 100644 index 00000000..e69de29b From a66ec8479e159e24413e9786793744d58705e313 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 18 Mar 2024 14:10:23 +0100 Subject: [PATCH 26/28] bugfix for vcf --- bin/vcf_collect.py | 69 ++++++++++++++++++++++++++++++++-------------- 1 file changed, 49 insertions(+), 20 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 7e988c1e..5b73a92e 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -65,7 +65,9 @@ def vcf_collect( gtf_df = build_gtf_dataframe(gtf) all_df = df.merge(gtf_df, how="left", left_on="CDS_LEFT_ID", right_on="Transcript_id") - all_df[["PosA", "orig_start", "orig_end"]] = all_df[["PosA", "orig_start", "orig_end"]].fillna(0).astype(int) + all_df[["PosA", "orig_start", "orig_end"]] = ( + all_df[["PosA", "orig_start", "orig_end"]].fillna(0).astype(int) + ) all_df = all_df[ ((all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])) @@ -75,7 +77,9 @@ def vcf_collect( all_df.replace("", np.nan, inplace=True) all_df = all_df.drop_duplicates() - all_df[["exon_number", "transcript_version"]] = all_df[["exon_number", "transcript_version"]].replace(0, np.nan) + all_df[["exon_number", "transcript_version"]] = all_df[ + ["exon_number", "transcript_version"] + ].replace(0, np.nan) # Fill non-empty values within each group for 'exon_number' and 'transcript_version' all_df["exon_number"] = all_df.groupby("PosA")["exon_number"].transform( lambda x: x.fillna(method="ffill").fillna(method="bfill") @@ -116,8 +120,12 @@ def vcf_collect( ].drop_duplicates() all_df["CDS_RIGHT_ID"] = all_df["CDS_RIGHT_ID"].astype("str") all_df = all_df.merge(gtf_df, how="left", left_on="CDS_RIGHT_ID", right_on="Transcript_id") - all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].fillna(0) - all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].astype(int) + all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].fillna( + 0 + ) + all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].astype( + int + ) all_df = all_df[ ((all_df["PosB"] >= all_df["orig_start"]) & (all_df["PosB"] <= all_df["orig_end"])) | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) @@ -126,7 +134,9 @@ def vcf_collect( all_df[["PosA", "PosB"]] = all_df[["PosA", "PosB"]].replace(0, np.nan) all_df = all_df.replace("", np.nan) - all_df[["exon_number", "transcript_version"]] = all_df[["exon_number", "transcript_version"]].replace(0, np.nan) + all_df[["exon_number", "transcript_version"]] = all_df[ + ["exon_number", "transcript_version"] + ].replace(0, np.nan) # Fill non-empty values within each group for 'exon_number' and 'transcript_version' all_df["exon_number"] = all_df.groupby("PosB")["exon_number"].transform( lambda x: x.fillna(method="ffill").fillna(method="bfill") @@ -212,7 +222,9 @@ def parse_args(argv=None): type=Path, help="HGNC database.", ) - parser.add_argument("--sample", metavar="SAMPLE", type=Path, help="Sample name.", default="Sample") + parser.add_argument( + "--sample", metavar="SAMPLE", type=Path, help="Sample name.", default="Sample" + ) parser.add_argument( "--out", metavar="OUT", @@ -280,7 +292,11 @@ def build_fusioninspector_dataframe(file: str) -> pd.DataFrame: df["annots"] = ( df["annots"] .apply(convert_to_list) - .apply(lambda x: ",".join(map(str, x)) if isinstance(x, list) else str(x) if pd.notna(x) else "") + .apply( + lambda x: ( + ",".join(map(str, x)) if isinstance(x, list) else str(x) if pd.notna(x) else "" + ) + ) ) else: for i in [ @@ -334,9 +350,10 @@ def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame: Make all column headers uppercase. """ with open(fusionreport_file) as f: - from_html = [line.split('rows": [')[1] for line in f if 'name="fusion_list' in line] - expression = ast.literal_eval(from_html[0].split('], "tool')[0]) - fusion_report = pd.DataFrame.from_dict({k: [v] for k, v in expression.items()}) + from_html = [line.split('rows": ')[1] for line in f if 'name="fusion_list' in line] + tmp=str(from_html)[2:] + tmp2 = (tmp.split(', "tools": ')[0]) + fusion_report = pd.DataFrame(ast.literal_eval(tmp2)) if not "arriba" in fusion_report.columns: fusion_report["arriba"] = "" if not "fusioncatcher" in fusion_report.columns: @@ -356,12 +373,12 @@ def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame: concatenate_columns, axis=1 ) fusion_report.columns = fusion_report.columns.str.upper() - fusion_report["FOUND_DB"] = fusion_report["FOUND_DB"].apply(lambda x: ",".join(x)) + fusion_report["FOUND_DB"] = fusion_report["FOUND_DB"].apply(lambda x: ",".join(x) if len(x) > 0 else '') fusion_report[["GeneA", "GeneB"]] = fusion_report["FUSION"].str.split("--", expand=True) - return fusion_report[["FUSION", "GeneA", "GeneB", "TOOLS_HITS", "SCORE", "FOUND_DB", "FOUND_IN"]].set_index( - ["FUSION"] - ) + return fusion_report[ + ["FUSION", "GeneA", "GeneB", "TOOLS_HITS", "SCORE", "FOUND_DB", "FOUND_IN"] + ].set_index(["FUSION"]) def read_fusionreport_csv(file: str) -> pd.DataFrame: @@ -370,7 +387,9 @@ def read_fusionreport_csv(file: str) -> pd.DataFrame: for column in columns_to_iterate: if column not in df.columns: df[column] = "" - df[["starfusion", "arriba", "fusioncatcher"]] = df[["starfusion", "arriba", "fusioncatcher"]].astype("str") + df[["starfusion", "arriba", "fusioncatcher"]] = df[ + ["starfusion", "arriba", "fusioncatcher"] + ].astype("str") for index, row in df.iterrows(): for column in columns_to_iterate: cell_value = row[column] @@ -398,7 +417,9 @@ def read_fusionreport_csv(file: str) -> pd.DataFrame: df[["GeneA", "GeneB"]] = df["Fusion"].str.split("--", expand=True) df = df.set_index("Fusion") df.to_csv("tmp.csv") - return df[["GeneA", "GeneB", "ChromosomeA", "PosA", "StrandA", "ChromosomeB", "PosB", "StrandB"]] + return df[ + ["GeneA", "GeneB", "ChromosomeA", "PosA", "StrandA", "ChromosomeB", "PosB", "StrandB"] + ] def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: @@ -425,7 +446,9 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: df["Left_exon_number"] = df["Left_exon_number"].fillna(0).astype(int).astype(str) df["Right_exon_number"] = df["Right_exon_number"].fillna(0).astype(int).astype(str) df["Left_transcript_version"] = df["Left_transcript_version"].fillna(0).astype(int).astype(str) - df["Right_transcript_version"] = df["Right_transcript_version"].fillna(0).astype(int).astype(str) + df["Right_transcript_version"] = ( + df["Right_transcript_version"].fillna(0).astype(int).astype(str) + ) df["PosA"] = df["PosA"].fillna(0).astype(int).astype(str) df["PosB"] = df["PosB"].fillna(0).astype(int).astype(str) df["PROT_FUSION_TYPE"] = df["PROT_FUSION_TYPE"].replace(".", "nan") @@ -452,7 +475,9 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: f"EXON_NUMBER_A={row['Left_exon_number']};EXON_NUMBER_B={row['Right_exon_number']};" f"ANNOTATIONS={row['annots']}" ) - df.loc[index, "Sample"] = f"./1:{row['JunctionReadCount']}:{row['SpanningFragCount']}:{row['FFPM']}" + df.loc[index, "Sample"] = ( + f"./1:{row['JunctionReadCount']}:{row['SpanningFragCount']}:{row['FFPM']}" + ) return df @@ -497,7 +522,9 @@ def build_gtf_dataframe(file: str) -> pd.DataFrame: """ df = pd.read_csv(file, sep="\t") df[["fusion_dump", "Transcript_id"]] = df["transcript_id"].str.split("^", expand=True) - df[["orig_chromosome", "orig_start", "orig_end", "orig_dir"]] = df["orig_coord_info"].str.split(",", expand=True) + df[["orig_chromosome", "orig_start", "orig_end", "orig_dir"]] = df["orig_coord_info"].str.split( + ",", expand=True + ) return df[["Transcript_id", "transcript_version", "exon_number", "orig_start", "orig_end"]] @@ -511,7 +538,9 @@ def main(argv=None): or not args.fusionreport_csv or not args.hgnc ): - logger.error(f"The given input file {args.fusioninspector} or {args.fusionreport} was not found!") + logger.error( + f"The given input file {args.fusioninspector} or {args.fusionreport} was not found!" + ) sys.exit(2) vcf_collect( args.fusioninspector, From 3ec309015f0ce12c0c5d678075b00bfe19a30db8 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 18 Mar 2024 20:09:46 +0100 Subject: [PATCH 27/28] black without line limit --- bin/vcf_collect.py | 135 +++++++++++++++++++++++++++++++-------------- 1 file changed, 95 insertions(+), 40 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 5b73a92e..1decbe90 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -47,9 +47,14 @@ def vcf_collect( df_not_symbol = merged_df[merged_df["Left_ensembl_gene_id"].notna()] df_not_symbol = hgnc_df.merge( - df_not_symbol, how="right", left_on="ensembl_gene_id", right_on="Left_ensembl_gene_id" + df_not_symbol, + how="right", + left_on="ensembl_gene_id", + right_on="Left_ensembl_gene_id", + ) + df_symbol = hgnc_df.merge( + df_symbol, how="right", left_on="symbol", right_on="GeneA" ) - df_symbol = hgnc_df.merge(df_symbol, how="right", left_on="symbol", right_on="GeneA") df = pd.concat([df_not_symbol, df_symbol]) df = df.rename(columns={"hgnc_id": "Left_hgnc_id"}) @@ -57,20 +62,30 @@ def vcf_collect( df_not_symbol = df[df["Right_ensembl_gene_id"].notna()] df_not_symbol = hgnc_df.merge( - df_not_symbol, how="right", left_on="ensembl_gene_id", right_on="Right_ensembl_gene_id" + df_not_symbol, + how="right", + left_on="ensembl_gene_id", + right_on="Right_ensembl_gene_id", + ) + df_symbol = hgnc_df.merge( + df_symbol, how="right", left_on="symbol", right_on="GeneB" ) - df_symbol = hgnc_df.merge(df_symbol, how="right", left_on="symbol", right_on="GeneB") df = pd.concat([df_not_symbol, df_symbol]) df = df.rename(columns={"hgnc_id": "Right_hgnc_id"}) gtf_df = build_gtf_dataframe(gtf) - all_df = df.merge(gtf_df, how="left", left_on="CDS_LEFT_ID", right_on="Transcript_id") + all_df = df.merge( + gtf_df, how="left", left_on="CDS_LEFT_ID", right_on="Transcript_id" + ) all_df[["PosA", "orig_start", "orig_end"]] = ( all_df[["PosA", "orig_start", "orig_end"]].fillna(0).astype(int) ) all_df = all_df[ - ((all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])) + ( + (all_df["PosA"] >= all_df["orig_start"]) + & (all_df["PosA"] <= all_df["orig_end"]) + ) | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) ] @@ -84,9 +99,9 @@ def vcf_collect( all_df["exon_number"] = all_df.groupby("PosA")["exon_number"].transform( lambda x: x.fillna(method="ffill").fillna(method="bfill") ) - all_df["transcript_version"] = all_df.groupby("PosA")["transcript_version"].transform( - lambda x: x.fillna(method="ffill").fillna(method="bfill") - ) + all_df["transcript_version"] = all_df.groupby("PosA")[ + "transcript_version" + ].transform(lambda x: x.fillna(method="ffill").fillna(method="bfill")) all_df = all_df.rename(columns={"transcript_version": "Left_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Left_exon_number"}) @@ -119,15 +134,20 @@ def vcf_collect( ] ].drop_duplicates() all_df["CDS_RIGHT_ID"] = all_df["CDS_RIGHT_ID"].astype("str") - all_df = all_df.merge(gtf_df, how="left", left_on="CDS_RIGHT_ID", right_on="Transcript_id") - all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].fillna( - 0 - ) - all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].astype( - int + all_df = all_df.merge( + gtf_df, how="left", left_on="CDS_RIGHT_ID", right_on="Transcript_id" ) + all_df[["PosB", "orig_start", "orig_end"]] = all_df[ + ["PosB", "orig_start", "orig_end"] + ].fillna(0) + all_df[["PosB", "orig_start", "orig_end"]] = all_df[ + ["PosB", "orig_start", "orig_end"] + ].astype(int) all_df = all_df[ - ((all_df["PosB"] >= all_df["orig_start"]) & (all_df["PosB"] <= all_df["orig_end"])) + ( + (all_df["PosB"] >= all_df["orig_start"]) + & (all_df["PosB"] <= all_df["orig_end"]) + ) | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) ] @@ -141,9 +161,9 @@ def vcf_collect( all_df["exon_number"] = all_df.groupby("PosB")["exon_number"].transform( lambda x: x.fillna(method="ffill").fillna(method="bfill") ) - all_df["transcript_version"] = all_df.groupby("PosB")["transcript_version"].transform( - lambda x: x.fillna(method="ffill").fillna(method="bfill") - ) + all_df["transcript_version"] = all_df.groupby("PosB")[ + "transcript_version" + ].transform(lambda x: x.fillna(method="ffill").fillna(method="bfill")) all_df = all_df.rename(columns={"transcript_version": "Right_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Right_exon_number"}) @@ -285,16 +305,26 @@ def build_fusioninspector_dataframe(file: str) -> pd.DataFrame: df = pd.read_csv(file, sep="\t") df = df.rename(columns={"#FusionName": "FUSION"}) if not (df.empty): - df[["ChromosomeA", "PosA", "Strand1"]] = df["LeftBreakpoint"].str.split(":", expand=True) - df[["ChromosomeB", "PosB", "Strand2"]] = df["RightBreakpoint"].str.split(":", expand=True) - df[["LeftGeneName", "Left_ensembl_gene_id"]] = df["LeftGene"].str.split("^", expand=True) - df[["RightGeneName", "Right_ensembl_gene_id"]] = df["RightGene"].str.split("^", expand=True) + df[["ChromosomeA", "PosA", "Strand1"]] = df["LeftBreakpoint"].str.split( + ":", expand=True + ) + df[["ChromosomeB", "PosB", "Strand2"]] = df["RightBreakpoint"].str.split( + ":", expand=True + ) + df[["LeftGeneName", "Left_ensembl_gene_id"]] = df["LeftGene"].str.split( + "^", expand=True + ) + df[["RightGeneName", "Right_ensembl_gene_id"]] = df["RightGene"].str.split( + "^", expand=True + ) df["annots"] = ( df["annots"] .apply(convert_to_list) .apply( lambda x: ( - ",".join(map(str, x)) if isinstance(x, list) else str(x) if pd.notna(x) else "" + ",".join(map(str, x)) + if isinstance(x, list) + else str(x) if pd.notna(x) else "" ) ) ) @@ -320,7 +350,9 @@ def build_fusioninspector_dataframe(file: str) -> pd.DataFrame: return df.set_index(["FUSION"]) -def replace_value_with_column_name(row: pd.Series, value_to_replace: str, column_name: str) -> str: +def replace_value_with_column_name( + row: pd.Series, value_to_replace: str, column_name: str +) -> str: """ Replace a specific value in a row with the corresponding column name. """ @@ -350,9 +382,11 @@ def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame: Make all column headers uppercase. """ with open(fusionreport_file) as f: - from_html = [line.split('rows": ')[1] for line in f if 'name="fusion_list' in line] - tmp=str(from_html)[2:] - tmp2 = (tmp.split(', "tools": ')[0]) + from_html = [ + line.split('rows": ')[1] for line in f if 'name="fusion_list' in line + ] + tmp = str(from_html)[2:] + tmp2 = tmp.split(', "tools": ')[0] fusion_report = pd.DataFrame(ast.literal_eval(tmp2)) if not "arriba" in fusion_report.columns: fusion_report["arriba"] = "" @@ -369,12 +403,16 @@ def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame: fusion_report["starfusion"] = fusion_report[["starfusion"]].apply( replace_value_with_column_name, args=("true", "starfusion"), axis=1 ) - fusion_report["FOUND_IN"] = fusion_report[["arriba", "starfusion", "fusioncatcher"]].apply( - concatenate_columns, axis=1 - ) + fusion_report["FOUND_IN"] = fusion_report[ + ["arriba", "starfusion", "fusioncatcher"] + ].apply(concatenate_columns, axis=1) fusion_report.columns = fusion_report.columns.str.upper() - fusion_report["FOUND_DB"] = fusion_report["FOUND_DB"].apply(lambda x: ",".join(x) if len(x) > 0 else '') - fusion_report[["GeneA", "GeneB"]] = fusion_report["FUSION"].str.split("--", expand=True) + fusion_report["FOUND_DB"] = fusion_report["FOUND_DB"].apply( + lambda x: ",".join(x) if len(x) > 0 else "" + ) + fusion_report[["GeneA", "GeneB"]] = fusion_report["FUSION"].str.split( + "--", expand=True + ) return fusion_report[ ["FUSION", "GeneA", "GeneB", "TOOLS_HITS", "SCORE", "FOUND_DB", "FOUND_IN"] @@ -418,7 +456,16 @@ def read_fusionreport_csv(file: str) -> pd.DataFrame: df = df.set_index("Fusion") df.to_csv("tmp.csv") return df[ - ["GeneA", "GeneB", "ChromosomeA", "PosA", "StrandA", "ChromosomeB", "PosB", "StrandB"] + [ + "GeneA", + "GeneB", + "ChromosomeA", + "PosA", + "StrandA", + "ChromosomeB", + "PosB", + "StrandB", + ] ] @@ -445,7 +492,9 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: df["Right_hgnc_id"] = df["Right_hgnc_id"].fillna(0).astype(int).astype(str) df["Left_exon_number"] = df["Left_exon_number"].fillna(0).astype(int).astype(str) df["Right_exon_number"] = df["Right_exon_number"].fillna(0).astype(int).astype(str) - df["Left_transcript_version"] = df["Left_transcript_version"].fillna(0).astype(int).astype(str) + df["Left_transcript_version"] = ( + df["Left_transcript_version"].fillna(0).astype(int).astype(str) + ) df["Right_transcript_version"] = ( df["Right_transcript_version"].fillna(0).astype(int).astype(str) ) @@ -499,7 +548,9 @@ def write_vcf(df_to_print: pd.DataFrame, header: str, out_file: str) -> None: "FORMAT", "Sample", ] - ].to_csv(path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE) + ].to_csv( + path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE + ) with open(out_file, "r+") as f: content = f.read() @@ -521,11 +572,15 @@ def build_gtf_dataframe(file: str) -> pd.DataFrame: Build a DataFrame from GTF file converted in TSV, extracting relevant columns. """ df = pd.read_csv(file, sep="\t") - df[["fusion_dump", "Transcript_id"]] = df["transcript_id"].str.split("^", expand=True) - df[["orig_chromosome", "orig_start", "orig_end", "orig_dir"]] = df["orig_coord_info"].str.split( - ",", expand=True + df[["fusion_dump", "Transcript_id"]] = df["transcript_id"].str.split( + "^", expand=True ) - return df[["Transcript_id", "transcript_version", "exon_number", "orig_start", "orig_end"]] + df[["orig_chromosome", "orig_start", "orig_end", "orig_dir"]] = df[ + "orig_coord_info" + ].str.split(",", expand=True) + return df[ + ["Transcript_id", "transcript_version", "exon_number", "orig_start", "orig_end"] + ] def main(argv=None): From 2b6ff48b95e7b471fb7c5559e2a0a9ea1f8d91ec Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 19 Mar 2024 13:44:48 +0100 Subject: [PATCH 28/28] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 58e8c618..5ce3a28a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - fix bug when using parameter "whitelist" [#466](https://github.com/nf-core/rnafusion/pull/466) - fix VCF_COLLECT handling when a tool is absent from FUSIONREPORT report [#458](https://github.com/nf-core/rnafusion/pull/458) - fix VCF_COLLECT when fusioninspector output is empty but fusionreport is not [#465](https://github.com/nf-core/rnafusion/pull/465) +- fix VCF_COLLECT bug [#481](https://github.com/nf-core/rnafusion/pull/481) ### Removed
    Process Name \\", - " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
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    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
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    File typeConventional base calls