diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index 95549501..00000000 --- a/.editorconfig +++ /dev/null @@ -1,27 +0,0 @@ -root = true - -[*] -charset = utf-8 -end_of_line = lf -insert_final_newline = true -trim_trailing_whitespace = true -indent_size = 4 -indent_style = space - -[*.{yml,yaml}] -indent_size = 2 - -[*.json] -insert_final_newline = unset - -# These files are edited and tested upstream in nf-core/modules -[/modules/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset -indent_size = unset - -[/assets/email*] -indent_size = unset diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 7fe55006..00000000 --- a/.gitattributes +++ /dev/null @@ -1 +0,0 @@ -*.config linguist-language=nextflow diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml deleted file mode 100644 index 191fabd2..00000000 --- a/.github/.dockstore.yml +++ /dev/null @@ -1,6 +0,0 @@ -# Dockstore config version, not pipeline version -version: 1.2 -workflows: - - subclass: nfl - primaryDescriptorPath: /nextflow.config - publish: True diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md deleted file mode 100644 index 240a047c..00000000 --- a/.github/CONTRIBUTING.md +++ /dev/null @@ -1,128 +0,0 @@ -# nf-core/quantms: Contributing Guidelines - -Hi there! -Many thanks for taking an interest in improving nf-core/quantms. - -We try to manage the required tasks for nf-core/quantms using GitHub issues, you probably came to this page when creating one. -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 ;) - -> If you need help using or modifying nf-core/quantms then the best place to ask is on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Contribution workflow - -If you'd like to write some code for nf-core/quantms, the standard workflow is as follows: - -1. Check that there isn't already an issue about your idea in the [nf-core/quantms issues](https://github.com/nf-core/quantms/issues) to avoid duplicating work - * If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/quantms repository](https://github.com/nf-core/quantms) to your GitHub account -3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). -5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged - -If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). - -## Tests - -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. - -There are typically two types of tests that run: - -### Lint tests - -`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. - -If any failures or warnings are encountered, please follow the listed URL for more documentation. - -### Pipeline tests - -Each `nf-core` pipeline should be set up with a minimal set of test-data. -`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. -If there are any failures then the automated tests fail. -These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. - -## Patch - -:warning: Only in the unlikely and regretful event of a release happening with a bug. - -* On your own fork, make a new branch `patch` based on `upstream/master`. -* Fix the bug, and bump version (X.Y.Z+1). -* A PR should be made on `master` from patch to directly this particular bug. - -## Getting help - -For further information/help, please consult the [nf-core/quantms documentation](https://nf-co.re/quantms/usage) and don't hesitate to get in touch on the nf-core Slack [#quantms](https://nfcore.slack.com/channels/quantms) channel ([join our Slack here](https://nf-co.re/join/slack)). - -## Pipeline contribution conventions - -To make the nf-core/quantms code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. - -### Adding a new step - -If you wish to contribute a new step, please use the following coding standards: - -1. Define the corresponding input channel into your new process from the expected previous process channel -2. Write the process block (see below). -3. Define the output channel if needed (see below). -4. Add any new flags/options to `nextflow.config` with a default (see below). -5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`). -6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter). -7. Add sanity checks for all relevant parameters. -8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`. -9. Do local tests that the new code works properly and as expected. -10. Add a new test command in `.github/workflow/ci.yml`. -11. If applicable add a [MultiQC](https://https://multiqc.info/) module. -12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order. -13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`. - -### Default values - -Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. - -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. - -### Default processes resource requirements - -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. - -### Naming schemes - -Please use the following naming schemes, to make it easy to understand what is going where. - -* initial process channel: `ch_output_from_` -* intermediate and terminal channels: `ch__for_` - -### Nextflow version bumping - -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` - -### Software version reporting - -If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process. - -Add to the script block of the process, something like the following: - -```bash - --version &> v_.txt 2>&1 || true -``` - -or - -```bash - --help | head -n 1 &> v_.txt 2>&1 || true -``` - -You then need to edit the script `bin/scrape_software_versions.py` to: - -1. Add a Python regex for your tool's `--version` output (as in stored in the `v_.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1` -2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC. - -### 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). diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index f6c8f37c..00000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,63 +0,0 @@ ---- -name: Bug report -about: Report something that is broken or incorrect -labels: bug ---- - - - -## Check Documentation - -I have checked the following places for your error: - -- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) -- [ ] [nf-core/quantms pipeline documentation](https://nf-co.re/quantms/usage) - -## Description of the bug - - - -## Steps to reproduce - -Steps to reproduce the behaviour: - -1. Command line: -2. See error: - -## Expected behaviour - - - -## Log files - -Have you provided the following extra information/files: - -- [ ] The command used to run the pipeline -- [ ] The `.nextflow.log` file - -## System - -- Hardware: -- Executor: -- OS: -- Version - -## Nextflow Installation - -- Version: - -## Container engine - -- Engine: -- version: - -## Additional context - - diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml deleted file mode 100644 index 5ed54b9b..00000000 --- a/.github/ISSUE_TEMPLATE/config.yml +++ /dev/null @@ -1,8 +0,0 @@ -blank_issues_enabled: false -contact_links: - - name: Join nf-core - url: https://nf-co.re/join - about: Please join the nf-core community here - - name: "Slack #quantms channel" - url: https://nfcore.slack.com/channels/quantms - about: Discussion about the nf-core/quantms pipeline diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md deleted file mode 100644 index dea5ae09..00000000 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -name: Feature request -about: Suggest an idea for the nf-core/quantms pipeline -labels: enhancement ---- - - - -## Is your feature request related to a problem? Please describe - - - - - -## Describe the solution you'd like - - - -## Describe alternatives you've considered - - - -## Additional context - - diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md deleted file mode 100644 index d5d2afb4..00000000 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ /dev/null @@ -1,26 +0,0 @@ - - - -## PR checklist - -- [ ] This comment contains a description of changes (with reason). -- [ ] If you've fixed a bug or added code that should be tested, add tests! - - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/quantms/tree/master/.github/CONTRIBUTING.md) - - [ ] If necessary, also make a PR on the nf-core/quantms _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`). -- [ ] Usage Documentation in `docs/usage.md` is updated. -- [ ] Output Documentation in `docs/output.md` is updated. -- [ ] `CHANGELOG.md` is updated. -- [ ] `README.md` is updated (including new tool citations and authors/contributors). diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml deleted file mode 100644 index 692d0e06..00000000 --- a/.github/workflows/awsfulltest.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: nf-core AWS full size tests -# This workflow is triggered on published releases. -# It can be additionally triggered manually with GitHub actions workflow dispatch button. -# It runs the -profile 'test_full' on AWS batch - -on: - release: - types: [published] - workflow_dispatch: -jobs: - run-tower: - name: Run AWS full tests - if: github.repository == 'nf-core/quantms' - runs-on: ubuntu-latest - steps: - - name: Launch workflow via tower - uses: nf-core/tower-action@master - # 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 - - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/quantms/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/quantms/results-${{ github.sha }}" - } - profiles: '[ "test_full", "aws_tower" ]' - diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml deleted file mode 100644 index b542e0ec..00000000 --- a/.github/workflows/awstest.yml +++ /dev/null @@ -1,28 +0,0 @@ -name: nf-core AWS test -# This workflow can be triggered manually with the GitHub actions workflow dispatch button. -# It runs the -profile 'test' on AWS batch - -on: - workflow_dispatch: -jobs: - run-tower: - name: Run AWS tests - if: github.repository == 'nf-core/quantms' - runs-on: ubuntu-latest - steps: - - name: Launch workflow via tower - uses: nf-core/tower-action@master - - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - pipeline: ${{ github.repository }} - revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/quantms/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/quantms/results-${{ github.sha }}" - } - profiles: '[ "test", "aws_tower" ]' - diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml deleted file mode 100644 index 729c489a..00000000 --- a/.github/workflows/branch.yml +++ /dev/null @@ -1,46 +0,0 @@ -name: nf-core branch protection -# This workflow is triggered on PRs to master branch on the repository -# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` -on: - pull_request_target: - branches: [master] - -jobs: - test: - runs-on: ubuntu-latest - steps: - # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - - name: Check PRs - if: github.repository == 'nf-core/quantms' - run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/quantms ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] - - - # If the above check failed, post a comment on the PR explaining the failure - # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 - with: - message: | - ## This PR is against the `master` branch :x: - - * Do not close this PR - * Click _Edit_ and change the `base` to `dev` - * This CI test will remain failed until you push a new commit - - --- - - Hi @${{ github.event.pull_request.user.login }}, - - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. - The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. - - You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. - Note that even after this, the test will continue to show as failing until you push a new commit. - - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false - diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 96acbded..00000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,44 +0,0 @@ -name: nf-core CI -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors -on: - push: - branches: - - dev - pull_request: - release: - types: [published] - -# Uncomment if we need an edge release of Nextflow again -# env: NXF_EDGE: 1 - -jobs: - test: - name: Run workflow tests - # Only run on push if this is the nf-core dev branch (merged PRs) - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/quantms') }} - runs-on: ubuntu-latest - env: - NXF_VER: ${{ matrix.nxf_ver }} - NXF_ANSI_LOG: false - strategy: - matrix: - # Nextflow versions: check pipeline minimum and current latest - nxf_ver: ['21.04.0', ''] - test_profile: ['test', 'test_lfq'] - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - env: - CAPSULE_LOG: none - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - - 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 - # Remember that you can parallelise this by using strategy.matrix - run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile }},docker diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml deleted file mode 100644 index 3b448773..00000000 --- a/.github/workflows/linting.yml +++ /dev/null @@ -1,145 +0,0 @@ -name: nf-core linting -# This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines -on: - push: - pull_request: - release: - types: [published] - -jobs: - Markdown: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '10' - - name: Install markdownlint - run: npm install -g markdownlint-cli - - name: Run Markdownlint - run: markdownlint . - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 - with: - message: | - ## Markdown linting 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 `markdownlint-cli` - * On Mac: `brew install markdownlint-cli` - * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`) - * Fix the markdown errors - * Automatically: `markdownlint . --fix` - * Manually resolve anything left from `markdownlint .` - - Once you push these changes the test should pass, and you can hide this comment :+1: - - We highly recommend setting up markdownlint 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 - - EditorConfig: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v2 - - - uses: actions/setup-node@v1 - with: - node-version: '10' - - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker - - - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) - - YAML: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v1 - - uses: actions/setup-node@v1 - with: - node-version: '10' - - name: Install yaml-lint - run: npm install -g yaml-lint - - name: Run yaml-lint - run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 - with: - message: | - ## YAML linting 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 `yaml-lint` - * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`) - * Fix the markdown errors - * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")` - * Fix any reported errors in your YAML files - - Once you push these changes the test should pass, and you can hide this comment :+1: - - We highly recommend setting up yaml-lint 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 - - nf-core: - runs-on: ubuntu-latest - steps: - - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - env: - CAPSULE_LOG: none - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - - uses: actions/setup-python@v1 - with: - python-version: '3.6' - architecture: 'x64' - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core - - - name: Run nf-core lint - env: - GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - - name: Save PR number - if: ${{ always() }} - run: echo ${{ github.event.pull_request.number }} > PR_number.txt - - - name: Upload linting log file artifact - if: ${{ always() }} - uses: actions/upload-artifact@v2 - with: - name: linting-logs - path: | - lint_log.txt - lint_results.md - PR_number.txt - diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml deleted file mode 100644 index 90f03c6f..00000000 --- a/.github/workflows/linting_comment.yml +++ /dev/null @@ -1,29 +0,0 @@ - -name: nf-core linting comment -# This workflow is triggered after the linting action is complete -# It posts an automated comment to the PR, even if the PR is coming from a fork - -on: - workflow_run: - workflows: ["nf-core linting"] - -jobs: - test: - runs-on: ubuntu-latest - steps: - - name: Download lint results - uses: dawidd6/action-download-artifact@v2 - with: - workflow: linting.yml - - - name: Get PR number - id: pr_number - run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)" - - - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@v2 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - number: ${{ steps.pr_number.outputs.pr_number }} - path: linting-logs/lint_results.md - diff --git a/.gitignore b/.gitignore index b468c1ee..5b8dd1e1 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,6 @@ testing* *.pyc .idea/ .idea/* +*.log +/build/ +results*/ diff --git a/.markdownlint.yml b/.markdownlint.yml deleted file mode 100644 index 9e605fcf..00000000 --- a/.markdownlint.yml +++ /dev/null @@ -1,14 +0,0 @@ -# Markdownlint configuration file -default: true -line-length: false -ul-indent: - indent: 4 -no-duplicate-header: - siblings_only: true -no-inline-html: - allowed_elements: - - img - - p - - kbd - - details - - summary diff --git a/.nf-core.yml b/.nf-core.yml deleted file mode 100644 index 82c85b39..00000000 --- a/.nf-core.yml +++ /dev/null @@ -1,5 +0,0 @@ -lint: - files_unchanged: - - bin/scrape_software_versions.py - files_exist: - - conf/igenomes.config diff --git a/CHANGELOG.md b/CHANGELOG.md deleted file mode 100644 index 6ca497ce..00000000 --- a/CHANGELOG.md +++ /dev/null @@ -1,16 +0,0 @@ -# nf-core/quantms: Changelog - -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). - -## v1.0dev - [date] - -Initial release of nf-core/quantms, created with the [nf-core](https://nf-co.re/) template. - -### `Added` - -### `Fixed` - -### `Dependencies` - -### `Deprecated` diff --git a/CITATIONS.md b/CITATIONS.md index 31816cc4..339d5c35 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,23 +10,60 @@ ## Pipeline tools -* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [thermorawfileparser](https://pubmed.ncbi.nlm.nih.gov/31755270/) -* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Hulstaert N, Shofstahl J, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y. ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion. J Proteome Res. 2020 Jan 3;19(1):537-542. doi: 10.1021/acs.jproteome.9b00328. Epub 2019 Dec 6. PMID: 31755270; PMCID: PMC7116465. + +- [sdrf-pipelines](https://pubmed.ncbi.nlm.nih.gov/34615866/) + + > Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun. 2021 Oct 6;12(1):5854. doi: 10.1038/s41467-021-26111-3. PMID: 34615866; PMCID: PMC8494749. + +- [OpenMS](https://pubmed.ncbi.nlm.nih.gov/27312411/) + + > Röst HL., Sachsenberg T., Aiche S., Bielow C., Weisser H., Aicheler F., Andreotti S., Ehrlich HC., Gutenbrunner P., Kenar E., Liang X., Nahnsen S., Nilse L., Pfeuffer J., Rosenberger G., Rurik M., Schmitt U., Veit J., Walzer M., Wojnar D., Wolski WE., Schilling O., Choudhary JS, Malmström L., Aebersold R., Reinert K., Kohlbacher O. (2016). OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature methods, 13(9), 741–748. doi: 10.1038/nmeth.3959. PubMed PMID: 27575624; PubMed Central PMCID: PMC5617107. + +- [DIA-NN](https://pubmed.ncbi.nlm.nih.gov/31768060/) + + > Demichev V, Messner CB, Vernardis SI, Lilley KS, Ralser M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods. 2020 Jan;17(1):41-44. doi: 10.1038/s41592-019-0638-x. Epub 2019 Nov 25. PMID: 31768060; PMCID: PMC6949130. + +- [MSstats](https://www.ncbi.nlm.nih.gov/pubmed/24794931/) + + > Choi M., Chang CY., Clough T., Broudy D., Killeen T., MacLean B., Vitek O. (2014). MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics (Oxford, England), 30(17), 2524–2526. doi: 10.1093/bioinformatics/btu305. PubMed PMID: 24794931. + +- [Comet](https://www.ncbi.nlm.nih.gov/pubmed/23148064/) + + > Eng JK., Jahan TA., Hoopmann MR. (2013). Comet: an open-source MS/MS sequence database search tool. Proteomics, 13(1), 22–24. doi: 10.1002/pmic.201200439. PubMed PMID: 23148064 + +- [MS-GF+](https://www.ncbi.nlm.nih.gov/pubmed/25358478/) + + > Kim S., Pevzner PA. (2014). MS-GF+ makes progress towards a universal database search tool for proteomics. Nature communications, 5, 5277. doi: 10.1038/ncomms6277. PubMed PMID: 25358478; PubMed Central PMCID: PMC5036525 + +- [Epifany](https://pubmed.ncbi.nlm.nih.gov/31975601/) + + > Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O. EPIFANY: A Method for Efficient High-Confidence Protein Inference. J Proteome Res. 2020 Mar 6;19(3):1060-1072. doi: 10.1021/acs.jproteome.9b00566. Epub 2020 Feb 13. PMID: 31975601; PMCID: PMC7583457. + +- [Triqler](https://pubmed.ncbi.nlm.nih.gov/30482846/) + + > The M, Käll L. Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics. Mol Cell Proteomics. 2019 Mar;18(3):561-570. doi: 10.1074/mcp.RA118.001018. Epub 2018 Nov 27. PMID: 30482846; PMCID: PMC6398204. + +- [luciphor](https://pubmed.ncbi.nlm.nih.gov/23918812/) + > Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics. 2013 Nov;12(11):3409-19. doi: 10.1074/mcp.M113.028928. Epub 2013 Aug 5. PMID: 23918812; PMCID: PMC3820951. ## Software packaging/containerisation tools -* [Anaconda](https://anaconda.com) - > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. +- [Anaconda](https://anaconda.com) + + > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. + +- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) + + > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. -* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) - > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. +- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) -* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) - > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. + > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. -* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) +- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) -* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) - > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. +- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..b97de95f --- /dev/null +++ b/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = docs +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/README.md b/README.md index e2584de1..1b30c86b 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ -# ![nf-core/quantms](docs/images/nf-core-quantms_logo.png) +# ![nf-core/quantms](docs/images/nf-core-quantms_logo_light.png#gh-light-mode-only) ![nf-core/quantms](docs/images/nf-core-quantms_logo_dark.png#gh-dark-mode-only) -[![GitHub Actions CI Status](https://github.com/bigbio/quantms/workflows/nf-core%20CI/badge.svg)](https://github.com/bigbio/quantms/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/bigbio/quantms/workflows/nf-core%20linting/badge.svg)](https://github.com/bigbio/quantms/actions?query=workflow%3A%22nf-core+linting%22) +[![GitHub Actions CI Status](https://github.com/nf-core/quantms/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/quantms/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/quantms/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/quantms/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/quantms/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%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](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/) @@ -17,61 +17,117 @@ ## Introduction -**nf-core/quantms** is a bioinformatics best-practice analysis pipeline for Quantitiative Mass Spectrometry nf-core workflow. + +**nf-core/quantms** is a bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS). Currently, the workflow supports three major MS-based analytical methods: (i) Data dependant acquisition (DDA) label-free and Isobaric quantitation (e.g. TMT, iTRAQ); (ii) Data independent acquisition (DIA) label-free quantification (for details see our in-depth documentation on [quantms](https://quantms.readthedocs.io/en/latest/)). + +

+ nf-core/quantms workflow overview +

The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/quantms/results). + +On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/quantms/results). This gives you a hint on which reports and file types are produced by the pipeline in a standard run. The automatic continuous integration tests evaluate different workflows, including the peptide identification, quantification for LFQ, LFQ-DIA, and TMT test datasets. ## Pipeline summary -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +The quantms allows uses to perform analysis in three main type of analytical MS-based quantitative methods: DDA-LFQ, DDA-ISO, DIA-LFQ. Each of these workflows share some processes but also includes their own steps. In summary: + +DDA-LFQ: + +1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser)) +2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus) +3. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator) +4. Peptide identification FDR [`openms fdr tool`](https://github.com/ypriverol/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf) +5. Modification localization [`luciphor`](https://github.com/dfermin/lucXor) +6. Quantification: Feature detection [`proteomicsLFQ`](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_ProteomicsLFQ.html) +7. Protein inference and quantification [`proteomicsLFQ`](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_ProteomicsLFQ.html) +8. QC report generation [`pmultiqc`](https://github.com/bigbio/pmultiqc) +9. Normalization, imputation, significance testing with [`MSstats`](https://github.com/VitekLab/MSstats) + +DDA-ISO: + +1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser)) +2. Peptide identification using [`comet`](https://uwpr.github.io/Comet/) and/or [`msgf+`](https://github.com/MSGFPlus/msgfplus) +3. Re-scoring peptide identifications [`percolator`](https://github.com/percolator/percolator) +4. Peptide identification FDR [`openms fdr tool`](https://github.com/ypriverol/quantms/blob/dev/modules/local/openms/falsediscoveryrate/main.nf) +5. Modification localization [`luciphor`](https://github.com/dfermin/lucXor) +6. Extracts and normalizes isobaric labeling [`IsobaricAnalyzer`](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_IsobaricAnalyzer.html) +7. Protein inference [`ProteinInference`](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinInference.html) or [`Epifany`](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/UTILS_Epifany.html) for bayesian inference. +8. Protein Quantification [`ProteinQuantifier`](https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/nightly/html/TOPP_ProteinQuantifier.html) +9. QC report generation [`pmultiqc`](https://github.com/bigbio/pmultiqc) +10. Normalization, imputation, significance testing with [`MSstats`](https://github.com/VitekLab/MSstats) + +DIA-LFQ: + +1. RAW file conversion to mzML ([`thermorawfileparser`](https://github.com/compomics/ThermoRawFileParser)) +2. DIA-NN analysis [`dia-nn`](https://github.com/vdemichev/DiaNN/) +3. Generation of output files (msstats) +4. QC reports generation [`pmultiqc`](https://github.com/bigbio/pmultiqc) + +## Functionality overview + +A graphical overview of suggested routes through the pipeline depending on context can be seen below. + +

+ nf-core/quantms metro map +

## Quick Start -1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`) +1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`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 _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ 3. Download the pipeline and test it on a minimal dataset with a single command: - ```console - nextflow run nf-core/quantms -profile test, - ``` + ```console + nextflow run nf-core/quantms -profile test,YOURPROFILE --input project.sdrf.tsv --database protein.fasta --outdir + ``` - > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > * If you are using `singularity` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, it is highly recommended to use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to pre-download all of the required containers before running the pipeline and to set the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options to be able to store and re-use the images from a central location for future pipeline runs. - > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. + + > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. + > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. + > - If you are using `singularity` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. + > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + > + > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. + > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. + > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. + > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. 4. Start running your own analysis! - + - ```console - nextflow run nf-core/quantms -profile --input samplesheet.csv --genome GRCh37 - ``` + ```console + nextflow run nf-core/quantms -profile --input project.sdrf.tsv --database database.fasta --outdir + ``` ## Documentation -The nf-core/quantms pipeline comes with documentation about the pipeline [usage](https://nf-co.re/quantms/usage), [parameters](https://nf-co.re/quantms/parameters) and [output](https://nf-co.re/quantms/output). +The nf-core/quantms pipeline comes with a stand-alone [full documentation](https://quantms.readthedocs.io/en/latest/) including examples, benchmarks, and detailed explanation about the data analysis of proteomics data using quantms. In addition, quickstart documentation of the pipeline can be found in: [usage](https://nf-co.re/quantms/usage), [parameters](https://nf-co.re/quantms/parameters) and [output](https://nf-co.re/quantms/output). ## Credits -nf-core/quantms was originally written by Yasset Perez-Riverol. +nf-core/quantms was originally written by: Chengxin Dai ([@daichengxin](https://github.com/daichengxin)), Julianus Pfeuffer ([@jpfeuffer](https://github.com/jpfeuffer)) and Yasset Perez-Riverol ([@ypriverol](https://github.com/ypriverol)). We thank the following people for their extensive assistance in the development of this pipeline: +- Timo Sachsenberg ([@timosachsenberg](https://github.com/timosachsenberg)) +- Wang Hong ([@WangHong007](https://github.com/WangHong007)) + ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). -For further information or help, don't hesitate to get in touch on the [Slack `#quantms` channel](https://nfcore.slack.com/channels/quantms) (you can join with [this invite](https://nf-co.re/join/slack)). +For further information or help, don't hesitate to get in touch on the [Slack `#quantms` channel](https://nfcore.slack.com/channels/quantms) (you can join with [this invite](https://nf-co.re/join/slack)). In addition, users can get in touch using our [discussion forum](https://github.com/bigbio/quantms/discussions) ## Citations @@ -79,6 +135,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: diff --git a/assets/PXD000001.sdrf.tsv b/assets/PXD000001.sdrf.tsv deleted file mode 100644 index f9ca1631..00000000 --- a/assets/PXD000001.sdrf.tsv +++ /dev/null @@ -1,7 +0,0 @@ -Source Name Characteristics[organism] Characteristics[organism part] Characteristics[age] Characteristics[ancestry category] Characteristics[developmental stage] Characteristics[cell line] Characteristics[cell type] Characteristics[sex] Characteristics[mass] Characteristics[spiked compound] Characteristics[spiked compound 2] Characteristics[spiked compound 3] Characteristics[spiked compound 4] Characteristics[disease] Characteristics[biological replicate] Material Type assay name technology type comment[data file] comment[file uri] comment[technical replicate] comment[fraction identifier] comment[label] comment[instrument] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[modification parameters] comment[cleavage agent details] comment[dissociation method] comment[precursor mass tolerance] comment[fragment mass tolerance] Factor Value[spiked compound] Factor Value[spiked compound] Factor Value[spiked compound] Factor Value[spiked compound] -Sample 1 Dickeya chrysanthemi whole plant not available not available not available not applicable not available not applicable 1 SP=Yeast;CT=protein;AC=P00924;QY=10 SP=BOVIN;CT=protein;AC=P02769;QY=1 SP=RABIT;CT=protein;AC=P00489;QY=2 SP=BOVIN;CT=protein;AC=P62894;QY=1 not available 1 cell run 1 proteomic profiling by mass spectrometry TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw 1 1 TMT126 NT=LTQ Orbitrap Velos;AC=MS:1001742 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Methylthio;TA=C;MT=fixed;AC=UNIMOD:39 NT=TMT6plex;TA=K;MT=Fixed;AC=UNIMOD:737 NT=TMT6plex;PP=Any N-term;MT=Fixed;AC=UNIMOD:737 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 not available not available SP=Yeast;CT=protein;AC=P00924;QY=10 SP=BOVIN;CT=protein;AC=P02769;QY=1 SP=RABIT;CT=protein;AC=P00489;QY=2 SP=BOVIN;CT=protein;AC=P62894;QY=1 -Sample 2 Dickeya chrysanthemi whole plant not available not available not available not applicable not available not applicable 1 SP=Yeast;CT=protein;AC=P00924;QY=5 SP=BOVIN;CT=protein;AC=P02769;QY=2.5 SP=RABIT;CT=protein;AC=P00489;QY=2 SP=BOVIN;CT=protein;AC=P62894;QY=1 not available 1 cell run 1 proteomic profiling by mass spectrometry TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw 1 1 TMT127 NT=LTQ Orbitrap Velos;AC=MS:1001742 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Methylthio;TA=C;MT=fixed;AC=UNIMOD:39 NT=TMT6plex;TA=K;MT=Fixed;AC=UNIMOD:737 NT=TMT6plex;PP=Any N-term;MT=Fixed;AC=UNIMOD:737 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 not available not available SP=Yeast;CT=protein;AC=P00924;QY=5 SP=BOVIN;CT=protein;AC=P02769;QY=2.5 SP=RABIT;CT=protein;AC=P00489;QY=2 SP=BOVIN;CT=protein;AC=P62894;QY=1 -Sample 3 Dickeya chrysanthemi whole plant not available not available not available not applicable not available not applicable 1 SP=Yeast;CT=protein;AC=P00924;QY=2.5 SP=BOVIN;CT=protein;AC=P02769;QY=5 SP=RABIT;CT=protein;AC=P00489;QY=2 SP=BOVIN;CT=protein;AC=P62894;QY=1 not available 1 cell run 1 proteomic profiling by mass spectrometry TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw 1 1 TMT128 NT=LTQ Orbitrap Velos;AC=MS:1001742 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Methylthio;TA=C;MT=fixed;AC=UNIMOD:39 NT=TMT6plex;TA=K;MT=Fixed;AC=UNIMOD:737 NT=TMT6plex;PP=Any N-term;MT=Fixed;AC=UNIMOD:737 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 not available not available SP=Yeast;CT=protein;AC=P00924;QY=2.5 SP=BOVIN;CT=protein;AC=P02769;QY=5 SP=RABIT;CT=protein;AC=P00489;QY=2 SP=BOVIN;CT=protein;AC=P62894;QY=1 -Sample 4 Dickeya chrysanthemi whole plant not available not available not available not applicable not available not applicable 1 SP=Yeast;CT=protein;AC=P00924;QY=1 SP=BOVIN;CT=protein;AC=P02769;QY=10 SP=RABIT;CT=protein;AC=P00489;QY=2 SP=BOVIN;CT=protein;AC=P62894;QY=1 not available 1 cell run 1 proteomic profiling by mass spectrometry TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw 1 1 TMT129 NT=LTQ Orbitrap Velos;AC=MS:1001742 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Methylthio;TA=C;MT=fixed;AC=UNIMOD:39 NT=TMT6plex;TA=K;MT=Fixed;AC=UNIMOD:737 NT=TMT6plex;PP=Any N-term;MT=Fixed;AC=UNIMOD:737 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 not available not available SP=Yeast;CT=protein;AC=P00924;QY=1 SP=BOVIN;CT=protein;AC=P02769;QY=10 SP=RABIT;CT=protein;AC=P00489;QY=2 SP=BOVIN;CT=protein;AC=P62894;QY=1 -Sample 5 Dickeya chrysanthemi whole plant not available not available not available not applicable not available not applicable 1 SP=Yeast;CT=protein;AC=P00924;QY=2.5 SP=BOVIN;CT=protein;AC=P02769;QY=5 SP=RABIT;CT=protein;AC=P00489;QY=1 SP=BOVIN;CT=protein;AC=P62894;QY=1 not available 1 cell run 1 proteomic profiling by mass spectrometry TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw 1 1 TMT130 NT=LTQ Orbitrap Velos;AC=MS:1001742 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Methylthio;TA=C;MT=fixed;AC=UNIMOD:39 NT=TMT6plex;TA=K;MT=Fixed;AC=UNIMOD:737 NT=TMT6plex;PP=Any N-term;MT=Fixed;AC=UNIMOD:737 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 not available not available SP=Yeast;CT=protein;AC=P00924;QY=2.5 SP=BOVIN;CT=protein;AC=P02769;QY=5 SP=RABIT;CT=protein;AC=P00489;QY=1 SP=BOVIN;CT=protein;AC=P62894;QY=1 -Sample 6 Dickeya chrysanthemi whole plant not available not available not available not applicable not available not applicable 1 SP=Yeast;CT=protein;AC=P00924;QY=10 SP=BOVIN;CT=protein;AC=P02769;QY=1 SP=RABIT;CT=protein;AC=P00489;QY=1 SP=BOVIN;CT=protein;AC=P62894;QY=2 not available 1 cell run 1 proteomic profiling by mass spectrometry TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw 1 1 TMT131 NT=LTQ Orbitrap Velos;AC=MS:1001742 NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35 NT=Methylthio;TA=C;MT=fixed;AC=UNIMOD:39 NT=TMT6plex;TA=K;MT=Fixed;AC=UNIMOD:737 NT=TMT6plex;PP=Any N-term;MT=Fixed;AC=UNIMOD:737 AC=MS:1001313;NT=Trypsin NT=HCD;AC=PRIDE:0000590 not available not available SP=Yeast;CT=protein;AC=P00924;QY=10 SP=BOVIN;CT=protein;AC=P02769;QY=1 SP=RABIT;CT=protein;AC=P00489;QY=1 SP=BOVIN;CT=protein;AC=P62894;QY=2 diff --git a/assets/email_template.html b/assets/email_template.html deleted file mode 100644 index 7a622e34..00000000 --- a/assets/email_template.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - nf-core/quantms Pipeline Report - - -
- - - -

nf-core/quantms v${version}

-

Run Name: $runName

- -<% if (!success){ - out << """ -
-

nf-core/quantms execution completed unsuccessfully!

-

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

-

The full error message was:

- 
${errorReport}
-
- """ -} else { - out << """ -
- nf-core/quantms execution completed successfully! -
- """ -} -%> - -

The workflow was completed at $dateComplete (duration: $duration)

-

The command used to launch the workflow was as follows:

-
$commandLine
- -

Pipeline Configuration:

- - - <% out << summary.collect{ k,v -> "" }.join("\n") %> - -
$k
$v
- -

nf-core/quantms

-

https://github.com/nf-core/quantms

- -
- - - diff --git a/assets/email_template.txt b/assets/email_template.txt deleted file mode 100644 index b25faff4..00000000 --- a/assets/email_template.txt +++ /dev/null @@ -1,40 +0,0 @@ ----------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~\\ - |\\ | |__ __ / ` / \\ |__) |__ } { - | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, - `._,._,' - nf-core/quantms v${version} ----------------------------------------------------- - -Run Name: $runName - -<% if (success){ - out << "## nf-core/quantms execution completed successfully! ##" -} else { - out << """#################################################### -## nf-core/quantms execution completed unsuccessfully! ## -#################################################### -The exit status of the task that caused the workflow execution to fail was: $exitStatus. -The full error message was: - -${errorReport} -""" -} %> - - -The workflow was completed at $dateComplete (duration: $duration) - -The command used to launch the workflow was as follows: - - $commandLine - - - -Pipeline Configuration: ------------------------ -<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> - --- -nf-core/quantms -https://github.com/nf-core/quantms diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml deleted file mode 100644 index f3730512..00000000 --- a/assets/multiqc_config.yaml +++ /dev/null @@ -1,11 +0,0 @@ -report_comment: > - This report has been generated by the nf-core/quantms - analysis pipeline. For information about how to interpret these results, please see the - documentation. -report_section_order: - software_versions: - order: -1000 - nf-core-quantms-summary: - order: -1001 - -export_plots: true diff --git a/assets/nf-core-quantms_logo.png b/assets/nf-core-quantms_logo.png deleted file mode 100644 index 0f2d0b3c..00000000 Binary files a/assets/nf-core-quantms_logo.png and /dev/null differ diff --git a/assets/schema_input.json b/assets/schema_input.json deleted file mode 100644 index 22d7e10a..00000000 --- a/assets/schema_input.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/nf-core/quantms/master/assets/schema_input.json", - "title": "nf-core/quantms pipeline - params.input schema", - "description": "Schema for the file provided with params.input", - "type": "array", - "items": { - "type": "object", - "properties": { - "sample": { - "type": "string", - "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" - }, - "fastq_1": { - "type": "string", - "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 - } - ] - } - }, - "required": [ - "sample", - "fastq_1" - ] - } -} diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt deleted file mode 100644 index 81b7332d..00000000 --- a/assets/sendmail_template.txt +++ /dev/null @@ -1,53 +0,0 @@ -To: $email -Subject: $subject -Mime-Version: 1.0 -Content-Type: multipart/related;boundary="nfcoremimeboundary" - ---nfcoremimeboundary -Content-Type: text/html; charset=utf-8 - -$email_html - ---nfcoremimeboundary -Content-Type: image/png;name="nf-core-quantms_logo.png" -Content-Transfer-Encoding: base64 -Content-ID: -Content-Disposition: inline; filename="nf-core-quantms_logo.png" - -<% out << new File("$projectDir/assets/nf-core-quantms_logo.png"). - bytes. - encodeBase64(). - toString(). - tokenize( '\n' )*. - toList()*. - collate( 76 )*. - collect { it.join() }. - flatten(). - join( '\n' ) %> - -<% -if (mqcFile){ -def mqcFileObj = new File("$mqcFile") -if (mqcFileObj.length() < mqcMaxSize){ -out << """ ---nfcoremimeboundary -Content-Type: text/html; name=\"multiqc_report\" -Content-Transfer-Encoding: base64 -Content-ID: -Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\" - -${mqcFileObj. - bytes. - encodeBase64(). - toString(). - tokenize( '\n' )*. - toList()*. - collate( 76 )*. - collect { it.join() }. - flatten(). - join( '\n' )} -""" -}} -%> - ---nfcoremimeboundary-- diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index e3008952..00000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,115 +0,0 @@ -#!/usr/bin/env python - -# nf-core: Update the script to check the sdrf -# This script is based on the example at: https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv - -import os -import sys -import errno -import argparse -from sdrf_pipelines.sdrf.sdrf import SdrfDataFrame -from sdrf_pipelines.sdrf.sdrf_schema import MASS_SPECTROMETRY -import pandas as pd - -def parse_args(args=None): - Description = "Reformat nf-core/quantms sdrf file and check its contents." - Epilog = "Example usage: python validate_sdrf.py