diff --git a/.editorconfig b/.editorconfig index b6b3190..9b99008 100644 --- a/.editorconfig +++ b/.editorconfig @@ -22,3 +22,11 @@ indent_size = unset [/assets/email*] indent_size = unset + +# ignore Readme +[README.md] +indent_style = unset + +# ignore python +[*.{py}] +indent_style = unset diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index ef1b956..af85af0 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -4,36 +4,36 @@ name: nf-core AWS full size tests # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] - workflow_dispatch: + release: + types: [published] + workflow_dispatch: jobs: - run-tower: - name: Run AWS full tests - if: github.repository == 'nf-core/omicsgenetraitassociation' - runs-on: ubuntu-latest - steps: - - name: Launch workflow via tower - 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 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/omicsgenetraitassociation/work-${{ github.sha }} - parameters: | - { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/omicsgenetraitassociation/results-${{ github.sha }}" - } - profiles: test_full + run-tower: + name: Run AWS full tests + if: github.repository == 'nf-core/omicsgenetraitassociation' + runs-on: ubuntu-latest + steps: + - name: Launch workflow via tower + 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 + with: + workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/omicsgenetraitassociation/work-${{ github.sha }} + parameters: | + { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/omicsgenetraitassociation/results-${{ github.sha }}" + } + profiles: test_full - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json + - uses: actions/upload-artifact@v4 + with: + name: Tower debug log file + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 7f344b7..a6d8950 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -3,31 +3,31 @@ name: nf-core AWS test # It runs the -profile 'test' on AWS batch on: - workflow_dispatch: + workflow_dispatch: jobs: - run-tower: - name: Run AWS tests - if: github.repository == 'nf-core/omicsgenetraitassociation' - runs-on: ubuntu-latest - steps: - # Launch workflow using Tower CLI tool action - - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/omicsgenetraitassociation/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/omicsgenetraitassociation/results-test-${{ github.sha }}" - } - profiles: test + run-tower: + name: Run AWS tests + if: github.repository == 'nf-core/omicsgenetraitassociation' + runs-on: ubuntu-latest + steps: + # Launch workflow using Tower CLI tool action + - name: Launch workflow via tower + uses: seqeralabs/action-tower-launch@v2 + with: + workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} + access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} + compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/omicsgenetraitassociation/work-${{ github.sha }} + parameters: | + { + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/omicsgenetraitassociation/results-test-${{ github.sha }}" + } + profiles: test - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json + - uses: actions/upload-artifact@v4 + with: + name: Tower debug log file + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 694e90e..e5f0e6b 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -1,24 +1,24 @@ name: "Close user-tagged issues and PRs" on: - schedule: - - cron: "0 0 * * 0" # Once a week + schedule: + - cron: "0 0 * * 0" # Once a week jobs: - clean-up: - runs-on: ubuntu-latest - permissions: - issues: write - pull-requests: write - steps: - - uses: actions/stale@v7 - with: - stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." - stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." - close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." - days-before-stale: 30 - days-before-close: 20 - days-before-pr-close: -1 - any-of-labels: "awaiting-changes,awaiting-feedback" - exempt-issue-labels: "WIP" - exempt-pr-labels: "WIP" - repo-token: "${{ secrets.GITHUB_TOKEN }}" + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@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." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml new file mode 100644 index 0000000..2547eb6 --- /dev/null +++ b/.github/workflows/download_pipeline.yml @@ -0,0 +1,67 @@ +name: Test successful pipeline download with 'nf-core download' + +# Run the workflow when: +# - dispatched manually +# - when a PR is opened or reopened to master branch +# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. +on: + workflow_dispatch: + pull_request: + types: + - opened + branches: + - master + pull_request_target: + branches: + - master + +env: + NXF_ANSI_LOG: false + +jobs: + download: + runs-on: ubuntu-latest + steps: + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 + + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + architecture: "x64" + - uses: eWaterCycle/setup-singularity@v7 + with: + singularity-version: 3.8.3 + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install git+https://github.com/nf-core/tools.git@dev + + - name: Get the repository name and current branch set as environment variable + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + + - name: Download the pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./ + run: | + nf-core download ${{ env.REPO_LOWERCASE }} \ + --revision ${{ env.REPO_BRANCH }} \ + --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + --compress "none" \ + --container-system 'singularity' \ + --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-cache-utilisation 'amend' \ + --download-configuration + + - name: Inspect download + run: tree ./${{ env.REPOTITLE_LOWERCASE }} + + - name: Run the downloaded pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 9b25d06..5a89221 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -1,55 +1,89 @@ name: Fix linting from a comment on: - issue_comment: - types: [created] + issue_comment: + types: [created] jobs: - deploy: - # Only run if comment is on a PR with the main repo, and if it contains the magic keywords - if: > - contains(github.event.comment.html_url, '/pull/') && - contains(github.event.comment.body, '@nf-core-bot fix linting') && - github.repository == 'nf-core/omicsgenetraitassociation' - runs-on: ubuntu-latest - steps: - # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@v4 - with: - token: ${{ secrets.nf_core_bot_auth_token }} - - # Action runs on the issue comment, so we don't get the PR by default - # Use the gh cli to check out the PR - - name: Checkout Pull Request - run: gh pr checkout ${{ github.event.issue.number }} - env: - GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - - uses: actions/setup-node@v4 - - - name: Install Prettier - run: npm install -g prettier @prettier/plugin-php - - # Check that we actually need to fix something - - name: Run 'prettier --check' - id: prettier_status - run: | - if prettier --check ${GITHUB_WORKSPACE}; then - echo "result=pass" >> $GITHUB_OUTPUT - else - echo "result=fail" >> $GITHUB_OUTPUT - fi - - - name: Run 'prettier --write' - if: steps.prettier_status.outputs.result == 'fail' - run: prettier --write ${GITHUB_WORKSPACE} - - - name: Commit & push changes - if: steps.prettier_status.outputs.result == 'fail' - run: | - git config user.email "core@nf-co.re" - git config user.name "nf-core-bot" - git config push.default upstream - git add . - git status - git commit -m "[automated] Fix linting with Prettier" - git push + fix-linting: + # Only run if comment is on a PR with the main repo, and if it contains the magic keywords + if: > + contains(github.event.comment.html_url, '/pull/') && + contains(github.event.comment.body, '@nf-core-bot fix linting') && + github.repository == 'nf-core/omicsgenetraitassociation' + runs-on: ubuntu-latest + steps: + # Use the @nf-core-bot token to check out so we can push later + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + with: + token: ${{ secrets.nf_core_bot_auth_token }} + + # indication that the linting is being fixed + - name: React on comment + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: eyes + + # Action runs on the issue comment, so we don't get the PR by default + # Use the gh cli to check out the PR + - name: Checkout Pull Request + run: gh pr checkout ${{ github.event.issue.number }} + env: + GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} + + # Install and run pre-commit + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + with: + python-version: 3.11 + + - name: Install pre-commit + run: pip install pre-commit + + - name: Run pre-commit + id: pre-commit + run: pre-commit run --all-files + continue-on-error: true + + # indication that the linting has finished + - name: react if linting finished succesfully + if: steps.pre-commit.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: "+1" + + - name: Commit & push changes + id: commit-and-push + if: steps.pre-commit.outcome == 'failure' + run: | + git config user.email "core@nf-co.re" + git config user.name "nf-core-bot" + git config push.default upstream + git add . + git status + git commit -m "[automated] Fix code linting" + git push + + - name: react if linting errors were fixed + id: react-if-fixed + if: steps.commit-and-push.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: hooray + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: confused + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + issue-number: ${{ github.event.issue.number }} + body: | + @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. + See [CI log](https://github.com/nf-core/omicsgenetraitassociation/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 6ad3392..26a9bbb 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -1,68 +1,68 @@ name: release-announcements # Automatic release toot and tweet anouncements on: - release: - types: [published] - workflow_dispatch: + release: + types: [published] + workflow_dispatch: jobs: - toot: - runs-on: ubuntu-latest - steps: - - uses: rzr/fediverse-action@master - with: - access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} - host: "mstdn.science" # custom host if not "mastodon.social" (default) - # GitHub event payload - # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release - message: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + toot: + runs-on: ubuntu-latest + steps: + - uses: rzr/fediverse-action@master + with: + access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} + host: "mstdn.science" # custom host if not "mastodon.social" (default) + # GitHub event payload + # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release + message: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - Please see the changelog: ${{ github.event.release.html_url }} + Please see the changelog: ${{ github.event.release.html_url }} - send-tweet: - runs-on: ubuntu-latest + send-tweet: + runs-on: ubuntu-latest - steps: - - uses: actions/setup-python@v4 - with: - python-version: "3.10" - - name: Install dependencies - run: pip install tweepy==4.14.0 - - name: Send tweet - shell: python - run: | - import os - import tweepy + steps: + - uses: actions/setup-python@v5 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install tweepy==4.14.0 + - name: Send tweet + shell: python + run: | + import os + import tweepy - client = tweepy.Client( - access_token=os.getenv("TWITTER_ACCESS_TOKEN"), - access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), - consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), - consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), - ) - tweet = os.getenv("TWEET") - client.create_tweet(text=tweet) - env: - TWEET: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + client = tweepy.Client( + access_token=os.getenv("TWITTER_ACCESS_TOKEN"), + access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), + consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), + consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), + ) + tweet = os.getenv("TWEET") + client.create_tweet(text=tweet) + env: + TWEET: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - Please see the changelog: ${{ github.event.release.html_url }} - TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} - TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} - TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} - TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + Please see the changelog: ${{ github.event.release.html_url }} + TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} + TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} + TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} + TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} - bsky-post: - runs-on: ubuntu-latest - steps: - - uses: zentered/bluesky-post-action@v0.0.2 - with: - post: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + bsky-post: + runs-on: ubuntu-latest + steps: + - uses: zentered/bluesky-post-action@v0.1.0 + with: + post: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - Please see the changelog: ${{ github.event.release.html_url }} - env: - BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} - BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} - # + Please see the changelog: ${{ github.event.release.html_url }} + env: + BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} + BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} + # diff --git a/.gitpod.yml b/.gitpod.yml index acf7269..01179e3 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,21 +1,21 @@ image: nfcore/gitpod:latest tasks: - - name: Update Nextflow and setup pre-commit - command: | - pre-commit install --install-hooks - nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update + - name: unset JAVA_TOOL_OPTIONS + command: | + unset JAVA_TOOL_OPTIONS 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 - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code + 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 + - oderwat.indent-rainbow # Highlight indentation level + - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0c31cdb..46518b1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,10 @@ repos: - - repo: https://github.com/pre-commit/mirrors-prettier - rev: "v2.7.1" - hooks: - - id: prettier + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v3.1.0" + hooks: + - id: prettier + - repo: https://github.com/editorconfig-checker/editorconfig-checker.python + rev: "2.7.3" + hooks: + - id: editorconfig-checker + alias: ec diff --git a/CITATIONS.md b/CITATIONS.md index 83fb40b..20047c2 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,28 +10,28 @@ ## Pipeline tools -- [corrmeta](https://doi.org/10.1142/9789814447973_0023) +- [corrmeta](https://doi.org/10.1142/9789814447973_0023) - > Province MA. Meta-analyses of correlated genomic scans. Genet Epidemiol. 2005;29:274,#137. + > Province MA. Meta-analyses of correlated genomic scans. Genet Epidemiol. 2005;29:274,#137. ## Software packaging/containerisation tools -- [Anaconda](https://anaconda.com) +- [Anaconda](https://anaconda.com) - > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. + > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. -- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/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. + > 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) - > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. -- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) +- [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. + > 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/README.md b/README.md index a0d4d3f..efbfe8d 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ -# ![nf-core/omicsgenetraitassociation](docs/images/nf-core-omicsgenetraitassociation_logo_light.png#gh-light-mode-only) ![nf-core/omicsgenetraitassociation](docs/images/nf-core-omicsgenetraitassociation_logo_dark.png#gh-dark-mode-only) - +

+ + + nf-core/omicsgenetraitassociation + +

[![GitHub Actions CI Status](https://github.com/nf-core/omicsgenetraitassociation/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/omicsgenetraitassociation/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/omicsgenetraitassociation/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/omicsgenetraitassociation/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/omicsgenetraitassociation/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) @@ -67,12 +71,12 @@ nf-core/omicsgenetraitassociation was originally written by Woo Jung ([@wsjung]( Many thanks to others who have written parts of the pipeline or helped out along the way too, including (but not limited to): -- [Chase Mateusiak](https://github.com/cmatKhan) -- [Sandeep Acharya](https://github.com/sandeepacharya464) -- [Edward Kang](https://github.com/edwardkang0925) -- Lisa Liao -- Michael Brent -- Michael Province +- [Chase Mateusiak](https://github.com/cmatKhan) +- [Sandeep Acharya](https://github.com/sandeepacharya464) +- [Edward Kang](https://github.com/edwardkang0925) +- Lisa Liao +- Michael Brent +- Michael Province ## Contributions and Support diff --git a/docs/output.md b/docs/output.md index 7e70a72..1c05b93 100644 --- a/docs/output.md +++ b/docs/output.md @@ -37,17 +37,17 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d 1. Prepare gene-level trait-association P-values -- [PASCAL](#pascal) -- [MMAP](#mmap) +- [PASCAL](#pascal) +- [MMAP](#mmap) 2. Perform (correlated) Meta-Analysis -- [CMA](#cma) +- [CMA](#cma) 3. Enrichment Analyses -- [MEA](#mea) -- [GOEA](#mea) +- [MEA](#mea) +- [GOEA](#mea) ### PASCAL @@ -56,9 +56,9 @@ This step aggregates GWAS summary statistics P-values to gene-level scores using
Output files -- `pascal/` - - `pascal_out.tsv`: PASCAL gene-level P-values - - `manhattan_plot.png`: manhattan plot +- `pascal/` + - `pascal_out.tsv`: PASCAL gene-level P-values + - `manhattan_plot.png`: manhattan plot ### MMAP @@ -67,9 +67,9 @@ This step uses MMAP to perform linear mixed model analysis using gene expression
Output files -- `mmap/` - - `mmap/`: directory containing single-gene results - - `parsed_output_mmap_results.csv`: parsed output file +- `mmap/` + - `mmap/`: directory containing single-gene results + - `parsed_output_mmap_results.csv`: parsed output file ### CMA @@ -78,9 +78,9 @@ This step performs correlated meta-analysis using the CMA package. It provides a
Output files -- `cma/` - - `CMA_meta.csv`: file with meta p-value - - `tetrachor_sigma.txt`: tetrachoric correlations between input datasets +- `cma/` + - `CMA_meta.csv`: file with meta p-value + - `tetrachor_sigma.txt`: tetrachoric correlations between input datasets ### MEA @@ -89,19 +89,19 @@ This step performs module and gene ontology (GO) enrichment analyses. It provide
Output files -- `mea/` - - `master_summary_.csv`: master summary file with all enrichment analysis results +- `mea/` + - `master_summary_.csv`: master summary file with all enrichment analysis results ### Pipeline information
Output files -- `pipeline_info/` - - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - - Parameters used by the pipeline run: `params.json`. +- `pipeline_info/` + - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. + - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. + - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. + - Parameters used by the pipeline run: `params.json`.
diff --git a/docs/usage.md b/docs/usage.md index 7dfe117..61a7b3f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,5 +1,7 @@ # nf-core/omicsgenetraitassociation: Usage +## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/omicsgenetraitassociation/usage](https://nf-co.re/omicsgenetraitassociation/usage) + > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ ## Introduction @@ -124,28 +126,28 @@ They are loaded in sequence, so later profiles can overwrite earlier profiles. If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. -- `test` - - A profile with a complete configuration for automated testing - - Includes links to test data so needs no other parameters -- `docker` - - A generic configuration profile to be used with [Docker](https://docker.com/) -- `singularity` - - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) -- `podman` - - A generic configuration profile to be used with [Podman](https://podman.io/) -- `shifter` - - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) -- `charliecloud` - - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) -- `apptainer` - - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) -- `conda` - - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. +- `test` + - A profile with a complete configuration for automated testing + - Includes links to test data so needs no other parameters +- `docker` + - A generic configuration profile to be used with [Docker](https://docker.com/) +- `singularity` + - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/) +- `podman` + - A generic configuration profile to be used with [Podman](https://podman.io/) +- `shifter` + - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) +- `charliecloud` + - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `apptainer` + - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) +- `conda` + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. **Omicsgenetraitassociation specific profiles** -- `test` - - A minimal test profile for the full workflow +- `test` + - A minimal test profile for the full workflow ### `-resume` diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 083d586..151032b 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -24,7 +24,7 @@ class WorkflowMain { // // Validate parameters and print summary to screen // - public static void initialise(workflow, params, log) { + public static void initialise(workflow, params, log, args) { // Print workflow version and exit on --version if (params.version) { @@ -35,6 +35,8 @@ class WorkflowMain { // 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) { @@ -60,4 +62,16 @@ class WorkflowMain { } 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/WorkflowOmicsgenetraitassociation.groovy b/lib/WorkflowOmicsgenetraitassociation.groovy index 1f8c6ee..0d380fa 100755 --- a/lib/WorkflowOmicsgenetraitassociation.groovy +++ b/lib/WorkflowOmicsgenetraitassociation.groovy @@ -11,7 +11,6 @@ class WorkflowOmicsgenetraitassociation { // Check and validate parameters // public static void initialise(params, log) { - } // @@ -59,9 +58,12 @@ class WorkflowOmicsgenetraitassociation { 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 diff --git a/main.nf b/main.nf index 29ffe58..5e775a9 100644 --- a/main.nf +++ b/main.nf @@ -24,23 +24,23 @@ nextflow.enable.dsl = 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// include { validateParameters; paramsHelp } from 'plugin/nf-validation' +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) -// } +// 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 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} -// // Validate input parameters -// if (params.validate_params) { -// validateParameters() -// } +// Validate input parameters +if (params.validate_params) { + validateParameters() +} -// WorkflowMain.initialise(workflow, params, log) +WorkflowMain.initialise(workflow, params, log, args) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/modules.json b/modules.json index 5aa4b5d..843f0fd 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", + "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "4ab13872435962dadc239979554d13709e20bf29", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index f0c63f6..fcff255 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -1,7 +1,7 @@ name: custom_dumpsoftwareversions channels: - - conda-forge - - bioconda - - defaults + - conda-forge + - bioconda + - defaults dependencies: - - bioconda::multiqc=1.17 + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 7685b33..2c7c929 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,13 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // 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 ? +<<<<<<< HEAD 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" +======= + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" +>>>>>>> TEMPLATE input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test index eec1db1..b1e1630 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -31,7 +31,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { 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 index 4274ed5..0b190ee 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -1,27 +1,33 @@ { "Should run without failures": { "content": [ - { - "0": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ], - "1": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "2": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "mqc_yml": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "versions": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "yml": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ] - } + [ + "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": "2023-11-03T14:43:22.157011" + "timestamp": "2024-01-09T23:01:18.710682" } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index b9e8f92..255eada 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -7,20 +7,15 @@ nextflow_process { tag "modules_nfcore" tag "fastqc" - test("Single-Read") { + test("sarscov2 single-end [fastq]") { when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ + input[0] = Channel.of([ [ id: 'test', single_end:true ], - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) """ } } @@ -28,82 +23,189 @@ nextflow_process { then { assertAll ( { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. // looks like this:
    Mon 2 Oct 2023
    test.gz
    // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, - { assert path(process.out.html.get(0).get(1)).getText().contains("") }, - { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { 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") } + ) + } + } + + test("sarscov2 paired-end [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { 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") } + ) + } + } + + test("sarscov2 interleaved [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { 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") } + ) + } + } + + test("sarscov2 paired-end [bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { 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") } ) } } -// TODO -// // -// // Test with paired-end data -// // -// workflow test_fastqc_paired_end { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with interleaved data -// // -// workflow test_fastqc_interleaved { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with bam data -// // -// workflow test_fastqc_bam { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with multiple samples -// // -// workflow test_fastqc_multiple { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with custom prefix -// // -// workflow test_fastqc_custom_prefix { -// input = [ -// [ id:'mysample', single_end:true ], // meta map -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } + + test("sarscov2 multiple [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { 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") } + ) + } + } + + test("sarscov2 custom_prefix") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { 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") } + ) + } + } + + test("sarscov2 single-end [fastq] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id: 'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { 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() } + ) + } + } + } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 636a32c..5d624bb 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,10 +1,20 @@ { + "sarscov2 single-end [fastq] - stub": { + "content": [ + [ + "test.html", + "test.zip", + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2024-01-17T18:40:57.254299" + }, "versions": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2023-10-09T23:40:54+0000" + "timestamp": "2024-01-17T18:36:50.033627" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index bc0bdb5..c31ddc2 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,7 @@ name: multiqc channels: - - conda-forge - - bioconda - - defaults + - conda-forge + - bioconda + - defaults dependencies: - - bioconda::multiqc=1.18 + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 00cc48d..1b9f7c4 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:1.18--pyhdfd78af_0' : - 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -43,7 +43,7 @@ process MULTIQC { stub: """ - touch multiqc_data + mkdir multiqc_data touch multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f1aa660..7943322 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,59 +1,58 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] + - multiqc: + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + licence: ["GPL-3.0-or-later"] input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - report: + type: file + description: MultiQC report file + pattern: "multiqc_report.html" + - data: + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" maintainers: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index c2dad21..d0438ed 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -7,12 +7,9 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" - test("MULTIQC: FASTQC") { + test("sarscov2 single-end [fastqc]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -26,20 +23,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } ) } } - test("MULTIQC: FASTQC and a config file") { + test("sarscov2 single-end [fastqc] [config]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -53,9 +47,35 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { 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() } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap new file mode 100644 index 0000000..d37e730 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:02:49.911994" + }, + "sarscov2 single-end [fastqc] - stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:03:14.524346" + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 72a3578..2fbba6e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -47,7 +47,6 @@ params { config_profile_contact = null config_profile_url = null - // Max resource options // Defaults only, expecting to be overwritten max_memory = '128.GB' @@ -75,7 +74,7 @@ try { } // Load nf-core/omicsgenetraitassociation custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! +// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! // try { // includeConfig "${params.custom_config_base}/pipeline/omicsgenetraitassociation.config" // } catch (Exception e) { @@ -95,6 +94,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + channels = ['conda-forge', 'bioconda', 'defaults'] apptainer.enabled = false } mamba { @@ -151,6 +151,8 @@ profiles { charliecloud { charliecloud.enabled = true conda.enabled = false +<<<<<<< HEAD +======= docker.enabled = false singularity.enabled = false podman.enabled = false @@ -161,6 +163,7 @@ profiles { apptainer.enabled = true apptainer.autoMounts = true conda.enabled = false +>>>>>>> TEMPLATE docker.enabled = false singularity.enabled = false podman.enabled = false @@ -189,12 +192,10 @@ plugins { id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } -//// Load igenomes.config if required -//if (!params.igenomes_ignore) { -// includeConfig 'conf/igenomes.config' -//} else { -// params.genomes = [:] -//} +// Nextflow plugins +plugins { + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. diff --git a/nextflow_schema.json b/nextflow_schema.json index 6ef914e..b865a9f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -206,7 +206,14 @@ "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"], + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], "hidden": true }, "email_on_fail": { diff --git a/workflows/omicsgenetraitassociation.nf b/workflows/omicsgenetraitassociation.nf index 1d28997..32792b6 100644 --- a/workflows/omicsgenetraitassociation.nf +++ b/workflows/omicsgenetraitassociation.nf @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation' +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) def citation = '\n' + WorkflowMain.citation(workflow) + '\n' @@ -15,16 +15,16 @@ log.info logo + paramsSummaryLog(workflow) + citation WorkflowOmicsgenetraitassociation.initialise(params, log) -// /* -// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -// CONFIG FILES -// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -// */ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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) +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) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -32,25 +32,10 @@ WorkflowOmicsgenetraitassociation.initialise(params, log) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// -// MODULES: local modules -// -include { PASCAL } from '../modules/local/pascal' -include { MMAP } from '../modules/local/mmap/mmap' -include { MMAP_PARSE } from '../modules/local/mmap/mmap_parse' -include { PREPROCESS_PASCAL } from '../modules/local/mea/preprocess' -include { RUN_PASCAL } from '../modules/local/mea/pascal' -include { POSTPROCESS_PASCAL } from '../modules/local/mea/postprocess' -include { GO_ANALYSIS } from '../modules/local/mea/go_analysis' -include { MERGE_ORA_AND_SUMMARY } from '../modules/local/mea/merge_ora_and_summary' - // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -// include { INPUT_CHECK } from '../subworkflows/local/input_check' -include { PASCAL_SUBWORKFLOW } from '../subworkflows/local/pascal' -include { MMAP_SUBWORKFLOW } from '../subworkflows/local/mmap' -include { CMA_SUBWORKFLOW } from '../subworkflows/local/cma' +include { INPUT_CHECK } from '../subworkflows/local/input_check' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -61,9 +46,9 @@ include { CMA_SUBWORKFLOW } from '../subworkflows/local/cma' // // 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 { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -72,171 +57,57 @@ include { CMA_SUBWORKFLOW } from '../subworkflows/local/cma' */ // Info required for completion email and summary -// def multiqc_report = [] +def multiqc_report = [] workflow OMICSGENETRAITASSOCIATION { ch_versions = Channel.empty() - ch_mea_preprocess_input = Channel.empty() - - // - // Validate and parse samplesheet - // - // TODO: deal with additional sources - Channel.fromSamplesheet("input") - .multiMap{ sample, trait, pascal, twas, additional_sources -> - def num_additional_sources = 0 - if (additional_sources) { - num_additional_sources = additional_sources.countLines() - } - def meta = ["id": sample, "trait": trait] - pascal: [meta, pascal] - twas: [meta, twas] - num_additional_sources: [meta, num_additional_sources] - } - .set { ch_input } - // ch_input.pascal.view() - // ch_input.twas.view() - // ch_input.num_additional_sources.view() - // - // MODULE: PASCAL + // SUBWORKFLOW: Read in samplesheet, validate and stage input files // - PASCAL_SUBWORKFLOW ( - ch_input.pascal, - params.pascal_gene_annotation, - params.pascal_ref_panel + INPUT_CHECK ( + file(params.input) ) - ch_pascal_output = PASCAL_SUBWORKFLOW.out.pascal_output - ch_pascal_cma_format = PASCAL_SUBWORKFLOW.out.cma_format_output - ch_versions = ch_versions.mix(PASCAL_SUBWORKFLOW.out.versions) - - // ch_pascal_output.view() + 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 // - // SUBWORKFLOW: MMAP_SUBWORKFLOW + // MODULE: Run FastQC // - MMAP_SUBWORKFLOW ( - params.mmap_gene_list, - params.trait, - ch_input.twas, - params.mmap_pedigree_file, - params.mmap_cov_matrix_file + FASTQC ( + INPUT_CHECK.out.reads ) - ch_mmap_parsed = MMAP_SUBWORKFLOW.out.parsed_mmap_output - ch_mmap_cma_format = MMAP_SUBWORKFLOW.out.cma_format_output - ch_versions = ch_versions.mix(MMAP_SUBWORKFLOW.out.versions) - - // - // MODULE: run CMA - // + ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - // ch_pascal_cma_format.view() - // ch_mmap_cma_format.view() - - ch_cma_input_files = ch_pascal_cma_format - .mix(ch_mmap_cma_format) - .toList() - - CMA_SUBWORKFLOW ( - ch_cma_input_files, - params.trait, - [] + CUSTOM_DUMPSOFTWAREVERSIONS ( + ch_versions.unique().collectFile(name: 'collated_versions.yml') ) - ch_pval = CMA_SUBWORKFLOW.out.pval - .collect() - ch_versions = ch_versions.mix(CMA_SUBWORKFLOW.out.versions) // - // MODULE: PREPROCESSFORPASCAL + // MODULE: MultiQC // - ch_mea_preprocess_input = ch_pval - .multiMap{ pval -> - gene_score_file: pval - meta: tuple ( params.pipeline, params.trait, params.gene_col_name, params.pval_col_name) - } + workflow_summary = WorkflowOmicsgenetraitassociation.paramsSummaryMultiqc(workflow, summary_params) + ch_workflow_summary = Channel.value(workflow_summary) - ch_module_files = Channel.fromPath("${params.module_file_dir}/*.txt") - .map { module_file -> - tuple ( module_file.baseName, module_file) - } + methods_description = WorkflowOmicsgenetraitassociation.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) + ch_methods_description = Channel.value(methods_description) - ch_preprocess_input = ch_mea_preprocess_input.gene_score_file - .combine(ch_module_files) - .combine(ch_mea_preprocess_input.meta) - .multiMap { gene_score_file, module_id, module_file_dir, pipeline, trait, gene_col_name, pval_col_name -> - gene_score_file: gene_score_file - module_file: tuple (module_id, module_file_dir) - meta: tuple (pipeline, trait, gene_col_name, pval_col_name) - } + 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([])) - PREPROCESS_PASCAL ( - ch_preprocess_input + MULTIQC ( + ch_multiqc_files.collect(), + ch_multiqc_config.toList(), + ch_multiqc_custom_config.toList(), + ch_multiqc_logo.toList() ) - ch_mea_paths = PREPROCESS_PASCAL.out.paths - ch_mea_meta = PREPROCESS_PASCAL.out.meta - ch_versions = ch_versions.mix(PREPROCESS_PASCAL.out.versions) - - // - // MODULE: MEA PASCAL - // - RUN_PASCAL ( - ch_mea_paths, - ch_mea_meta - ) - - ch_pascal_paths = RUN_PASCAL.out.paths - ch_pascal_meta = RUN_PASCAL.out.meta - ch_versions = ch_versions.mix(RUN_PASCAL.out.versions) - - // - // MODULE: POSTPROCESS_PASCAL - // - POSTPROCESS_PASCAL ( - ch_pascal_paths, - ch_pascal_meta, - params.numtests, - params.alpha - ) - ch_postprocess_paths = POSTPROCESS_PASCAL.out.paths - ch_postprocess_meta = POSTPROCESS_PASCAL.out.meta - ch_versions = ch_versions.mix(POSTPROCESS_PASCAL.out.versions) - - // - // MODULE: GO analysis - // - GO_ANALYSIS ( - ch_postprocess_paths, - ch_postprocess_meta - ) - ch_go_paths = GO_ANALYSIS.out.paths - ch_go_meta = GO_ANALYSIS.out.meta - ch_versions = ch_versions.mix(GO_ANALYSIS.out.versions) - - // - // MODULE: MERGE_ORA_AND_SUMMARY - // TODO: each run of MERGE_ORA_AND_SUMMARY overwrites contents of summary_dir. should not happen - // - MERGE_ORA_AND_SUMMARY ( - ch_go_paths, - ch_go_meta - ) - ch_merge_summary_dir = MERGE_ORA_AND_SUMMARY.out.summary_dir - ch_merge_summary_files = MERGE_ORA_AND_SUMMARY.out.summary_files - ch_merge_meta = MERGE_ORA_AND_SUMMARY.out.meta - ch_merge_trait = MERGE_ORA_AND_SUMMARY.out.trait - - // ch_merge_summary_files.collect().view() - - // concatenate summary slices and write to master_summary_.csv - ch_master_summary = ch_merge_summary_files - .collectFile(name: "master_summary_${params.trait}.csv", - cache: false, - keepHeader: true, - skip: 1, - storeDir: "${params.outdir}/mea/" - ) + multiqc_report = MULTIQC.out.report.toList() } /* @@ -247,7 +118,7 @@ workflow OMICSGENETRAITASSOCIATION { workflow.onComplete { if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log) + NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) } NfcoreTemplate.dump_parameters(workflow, params) NfcoreTemplate.summary(workflow, params, log) @@ -256,6 +127,13 @@ workflow.onComplete { } } +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 💡") + } +} + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END
    Process Name \\", + " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls