Merge pull request #37 from CenterForMedicalGeneticsGhent/dev

Dev

Author: matthdsm

.devcontainer/devcontainer.json

@@ -0,0 +1,25 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "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"
+            },
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}

.gitattributes

@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -95,3 +95,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
+
+## GitHub Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,48 +2,53 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-  - type: markdown
-    attributes:
-      value: |
-        Before you post this issue, please check the documentation:
-
-        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-
   - type: textarea
     id: description
     attributes:
       label: Description of the bug
       description: A clear and concise description of what the bug is.
     validations:
       required: true
-
   - type: textarea
     id: command_used
     attributes:
       label: Command used and terminal output
-      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
       render: console
-      placeholder: |
-        $ nextflow run ...
+      placeholder: "$ nextflow run ...
+
 
         Some output where something broke
 
+        "
   - type: textarea
     id: files
     attributes:
       label: Relevant files
-      description: |
-        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
-        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
 
+        "
   - type: textarea
     id: system
     attributes:
       label: System information
-      description: |
-        * Nextflow version _(eg. 21.10.3)_
+      description: "* Nextflow version _(eg. 22.10.1)_
+
         * Hardware _(eg. HPC, Desktop, Cloud)_
+
         * Executor _(eg. slurm, local, awsbatch)_
+
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing _(eg. 1.1, 1.5, 1.8.2)_
+
+        * Version of CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing _(eg. 1.1,
+        1.5, 1.8.2)_
+
+        "

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,6 +1,7 @@
 name: Feature request
-description: Suggest an idea for the cmgg-preprocessing pipeline
-labels: enhancement
+description: Suggest an idea for the CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing pipeline
+labels:
+  - enhancement
 body:
   - type: textarea
     id: description

.github/workflows/ci.yml

@@ -10,6 +10,8 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  AWS_ACCESS_KEY_ID: ${{ secrets.UGENT_S3_ACCESS_KEY }}
+  AWS_SECRET_ACCESS_KEY: ${{ secrets.UGENT_S3_SECRET_KEY }}
 
 jobs:
   test:
@@ -20,8 +22,18 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "21.10.3"
-          - "latest-everything"
+          - "22.10.4"
+          #- "latest-everything"
+        test:
+          - "test_flowcell"
+          #- "test_fastq"
+          #- "test_cram"
+        aligner:
+          #- "bowtie2"
+          - "bwamem"
+          #- "bwamem2"
+          #- "dragmap"
+          #- "snap"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -33,4 +45,4 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test }},docker  --aligner ${{ matrix.aligner }} --outdir ./results

.github/workflows/linting.yml

@@ -4,6 +4,8 @@ name: nf-core linting
 # that the code meets the nf-core guidelines.
 on:
   push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -12,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -25,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -38,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -50,12 +52,17 @@ jobs:
         with:
           message: |
             ## Python linting (`black`) is failing
+
             To keep the code consistent with lots of contributors, we run automated code consistency checks.
             To fix this CI test, please run:
+
             * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
             * Fix formatting errors in your pipeline: `black .`
+
             Once you push these changes the test should pass, and you can hide this comment :+1:
+
             We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
@@ -64,20 +71,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.7"
           architecture: "x64"
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
       - name: Run nf-core lint
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
@@ -91,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

.gitignore

@@ -1,8 +1,10 @@
 .nextflow*
+.nf-test
 work/
 data/
 results/
 .DS_Store
 testing/
 testing*
 *.pyc
+null

.nf-core.yml

@@ -1,23 +1,19 @@
 repository_type: pipeline
 lint:
   files_exist:
-    - assets/nf-core-preprocessing_logo_light.png
-    - assets/nf-core-preprocessing_logo_dark.png
-    - docs/images/nf-core-preprocessing_logo_light.png
-    - docs/images/nf-core-preprocessing_logo_dark.png
+    - .github/workflows/awsfulltest.yml
+    - .github/workflows/awstest.yml
+    - assets/nf-core-nf-cmgg-preprocessing_logo_dark.png
+    - assets/nf-core-nf-cmgg-preprocessing_logo_light.png
+    - conf/test_full.config
+    - docs/images/nf-core-nf-cmgg-preprocessing_logo_dark.png
+    - docs/images/nf-core-nf-cmgg-preprocessing_logo_light.png
   files_unchanged:
-    - .github/CONTRIBUTING.md
     - .github/ISSUE_TEMPLATE/feature_request.yml
-    - .github/ISSUE_TEMPLATE/bug_report.yml
     - .github/PULL_REQUEST_TEMPLATE.md
-    - .github/workflows/branch.yml
     - .github/workflows/linting.yml
-    - assets/email_template.html
-    - assets/email_template.txt
-    - assets/sendmail_template.txt
+    - .gitignore
     - docs/README.md
-    - lib/NfcoreTemplate.groovy
-    - .prettierignore
   nextflow_config:
     - manifest.name
     - manifest.homePage

.prettierignore

@@ -1,5 +1,6 @@
 email_template.html
-adaptivecard_template.json
+adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/
@@ -8,3 +9,4 @@ results/
 testing/
 testing*
 *.pyc
+bin/

CHANGELOG.md

@@ -3,7 +3,11 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.1
+## v1.0.2dev
+
+- Add `unaligned` denominator to unaligned samples
+
+## v1.0.1
 
 - Updated modules
 

README.md

@@ -2,7 +2,7 @@
 
 [![GitHub Actions CI Status](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/workflows/nf-core%20CI/badge.svg)](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/workflows/nf-core%20linting/badge.svg)](https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing/actions?query=workflow%3A%22nf-core+linting%22)
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.4-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 
 ## Introduction
 
@@ -22,7 +22,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.4`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.