diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index b290e09..97c8c97 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,20 +1,20 @@ { "name": "nfcore", - "image": "nfcore/gitpod:latest", - "remoteUser": "gitpod", - "runArgs": ["--privileged"], + "image": "nfcore/devcontainer:latest", - // Configure tool-specific properties. - "customizations": { - // Configure properties specific to VS Code. - "vscode": { - // Set *default* container specific settings.json values on container create. - "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python" - }, + "remoteUser": "root", + "privileged": true, - // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } + "remoteEnv": { + // Workspace path on the host for mounting with docker-outside-of-docker + "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}" + }, + + "onCreateCommand": "./.devcontainer/setup.sh", + + "hostRequirements": { + "cpus": 4, + "memory": "16gb", + "storage": "32gb" } } diff --git a/.editorconfig b/.editorconfig deleted file mode 100644 index 6d9b74c..0000000 --- a/.editorconfig +++ /dev/null @@ -1,37 +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 - -[*.{md,yml,yaml,html,css,scss,js}] -indent_size = 2 - -# 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 -[/subworkflows/nf-core/**] -charset = unset -end_of_line = unset -insert_final_newline = unset -trim_trailing_whitespace = unset -indent_style = unset - -[/assets/email*] -indent_size = unset - -# ignore python and markdown -[*.{py,md}] -indent_style = unset - -# ignore ro-crate metadata files -[**/ro-crate-metadata.json] -insert_final_newline = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index a3f2fb5..2cf6f3c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,23 +1,20 @@ -# `nf-core/postprocessing`: Contributing Guidelines +# `Clinical-Genomics/oncorefiner`: Contributing Guidelines Hi there! -Many thanks for taking an interest in improving nf-core/postprocessing. +Many thanks for taking an interest in improving Clinical-Genomics/oncorefiner. -We try to manage the required tasks for nf-core/postprocessing using GitHub issues, you probably came to this page when creating one. +We try to manage the required tasks for Clinical-Genomics/oncorefiner 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 ;) -> [!NOTE] -> If you need help using or modifying nf-core/postprocessing then the best place to ask is on the nf-core Slack [#postprocessing](https://nfcore.slack.com/channels/postprocessing) channel ([join our Slack here](https://nf-co.re/join/slack)). - ## Contribution workflow -If you'd like to write some code for nf-core/postprocessing, the standard workflow is as follows: +If you'd like to write some code for Clinical-Genomics/oncorefiner, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [nf-core/postprocessing issues](https://github.com/nf-core/postprocessing/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/postprocessing repository](https://github.com/nf-core/postprocessing) to your GitHub account +1. Check that there isn't already an issue about your idea in the [Clinical-Genomics/oncorefiner issues](https://github.com/Clinical-Genomics/oncorefiner/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 [Clinical-Genomics/oncorefiner repository](https://github.com/Clinical-Genomics/oncorefiner) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) 4. Use `nf-core pipelines 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 @@ -59,13 +56,9 @@ These tests are run both with the latest available version of `Nextflow` and als - Fix the bug, and bump version (X.Y.Z+1). - Open a pull-request from `patch` to `main`/`master` with the changes. -## Getting help - -For further information/help, please consult the [nf-core/postprocessing documentation](https://nf-co.re/postprocessing/usage) and don't hesitate to get in touch on the nf-core Slack [#postprocessing](https://nfcore.slack.com/channels/postprocessing) channel ([join our Slack here](https://nf-co.re/join/slack)). - ## Pipeline contribution conventions -To make the `nf-core/postprocessing` 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. +To make the `Clinical-Genomics/oncorefiner` 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 @@ -78,7 +71,7 @@ If you wish to contribute a new step, please use the following coding standards: 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. -8. If applicable, add a new test command in `.github/workflow/ci.yml`. +8. If applicable, add a new test in the `tests` directory. 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. @@ -115,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes To get started: -- Open the repo in [Codespaces](https://github.com/nf-core/postprocessing/codespaces) +- Open the repo in [Codespaces](https://github.com/Clinical-Genomics/oncorefiner/codespaces) - Tools installed - nf-core - Nextflow diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 203d96b..f33a0d5 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -2,13 +2,6 @@ name: Bug report description: Report something that is broken or incorrect labels: bug body: - - type: markdown - attributes: - value: | - Before you post this issue, please check the documentation: - - - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - - [nf-core/postprocessing pipeline documentation](https://nf-co.re/postprocessing/usage) - type: textarea id: description attributes: @@ -46,4 +39,4 @@ body: * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ - * Version of nf-core/postprocessing _(eg. 1.1, 1.5, 1.8.2)_ + * Version of Clinical-Genomics/oncorefiner _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 55ba395..0086358 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,7 +1 @@ -contact_links: - - name: Join nf-core - url: https://nf-co.re/join - about: Please join the nf-core community here - - name: "Slack #postprocessing channel" - url: https://nfcore.slack.com/channels/postprocessing - about: Discussion about the nf-core/postprocessing pipeline +blank_issues_enabled: true diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index bc81a63..ef575e1 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.yml +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -1,5 +1,5 @@ name: Feature request -description: Suggest an idea for the nf-core/postprocessing pipeline +description: Suggest an idea for the Clinical-Genomics/oncorefiner pipeline labels: enhancement body: - type: textarea diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index ff926f4..3f769a8 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,22 +1,21 @@ ## 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/postprocessing/tree/master/.github/CONTRIBUTING.md) -- [ ] If necessary, also make a PR on the nf-core/postprocessing _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/Clinical-Genomics/oncorefiner/tree/master/.github/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml deleted file mode 100644 index cdd956e..0000000 --- a/.github/workflows/awsfulltest.yml +++ /dev/null @@ -1,48 +0,0 @@ -name: nf-core AWS full size tests -# This workflow is triggered on PRs opened against the main/master branch. -# It can be additionally triggered manually with GitHub actions workflow dispatch button. -# It runs the -profile 'test_full' on AWS batch - -on: - workflow_dispatch: - pull_request_review: - types: [submitted] - release: - types: [published] - -jobs: - run-platform: - name: Run AWS full tests - # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered - if: github.repository == 'nf-core/postprocessing' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' - runs-on: ubuntu-latest - steps: - - name: Set revision variable - id: revision - run: | - echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT" - - - name: Launch workflow via Seqera Platform - 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: ${{ steps.revision.outputs.revision }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/postprocessing/work-${{ steps.revision.outputs.revision }} - parameters: | - { - "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/postprocessing/results-${{ steps.revision.outputs.revision }}" - } - profiles: test_full - - - uses: actions/upload-artifact@v4 - with: - name: Seqera Platform debug log file - path: | - seqera_platform_action_*.log - seqera_platform_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml deleted file mode 100644 index f725c81..0000000 --- a/.github/workflows/awstest.yml +++ /dev/null @@ -1,33 +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-platform: - name: Run AWS tests - if: github.repository == 'nf-core/postprocessing' - runs-on: ubuntu-latest - steps: - # Launch workflow using Seqera Platform CLI tool action - - name: Launch workflow via Seqera Platform - 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/postprocessing/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/postprocessing/results-test-${{ github.sha }}" - } - profiles: test - - - uses: actions/upload-artifact@v4 - with: - name: Seqera Platform debug log file - path: | - seqera_platform_action_*.log - seqera_platform_action_*.json diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 17aa175..3582d31 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,9 +13,9 @@ jobs: steps: # PRs to the nf-core repo main/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/postprocessing' + if: github.repository == 'Clinical-Genomics/oncorefiner' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/postprocessing ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == Clinical-Genomics/oncorefiner ]] && [[ $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 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index c4a597f..0000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,88 +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] - workflow_dispatch: - -env: - NXF_ANSI_LOG: false - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - -concurrency: - group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: true - -jobs: - test: - name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/postprocessing') }}" - runs-on: ubuntu-latest - strategy: - matrix: - NXF_VER: - - "24.04.2" - - "latest-everything" - profile: - - "conda" - - "docker" - - "singularity" - test_name: - - "test" - isMaster: - - ${{ github.base_ref == 'master' }} - # Exclude conda and singularity on dev - exclude: - - isMaster: false - profile: "conda" - - isMaster: false - profile: "singularity" - steps: - - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - with: - fetch-depth: 0 - - - name: Set up Nextflow - uses: nf-core/setup-nextflow@v2 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Set up Apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda - - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - - name: Clean up Disk space - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" - continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} - run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 0b6b1f2..6adb0ff 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 + - uses: actions/stale@5f858e3efba33a5ca4407a664cc011ad407f2008 # v10 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index ab06316..45884ff 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -12,14 +12,6 @@ on: required: true default: "dev" pull_request: - types: - - opened - - edited - - synchronize - branches: - - main - - master - pull_request_target: branches: - main - master @@ -52,9 +44,9 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.12" + python-version: "3.14" architecture: "x64" - name: Setup Apptainer @@ -65,7 +57,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git@dev + pip install git+https://github.com/nf-core/tools.git - name: Make a cache directory for the container images run: | @@ -120,6 +112,7 @@ jobs: echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" - name: Compare container image counts + id: count_comparison run: | if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} @@ -132,3 +125,10 @@ jobs: else echo "The pipeline can be downloaded successfully!" fi + + - name: Upload Nextflow logfile for debugging purposes + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 + with: + name: nextflow_logfile.txt + path: .nextflow.log* + include-hidden-files: true diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml deleted file mode 100644 index f159f65..0000000 --- a/.github/workflows/fix-linting.yml +++ /dev/null @@ -1,89 +0,0 @@ -name: Fix linting from a comment -on: - issue_comment: - types: [created] - -jobs: - 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/postprocessing' - runs-on: ubuntu-latest - steps: - # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.12" - - - 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/postprocessing/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index dbd52d5..20aac9b 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -3,46 +3,27 @@ name: nf-core linting # It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: - push: - branches: - - dev pull_request: release: types: [published] jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - - name: Set up Python 3.12 - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.12" - - - name: Install pre-commit - run: pip install pre-commit - - - name: Run pre-commit - run: pre-commit run --all-files - - nf-core: + lint: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6 with: - python-version: "3.12" + python-version: "3.14" architecture: "x64" - name: read .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.1.0 + uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml @@ -50,8 +31,12 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip + pip install pre-commit pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + - name: Run pre-commit + run: pre-commit run --all-files + - name: Run nf-core pipelines lint if: ${{ github.base_ref != 'master' }} env: @@ -74,7 +59,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 + uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 95b6b6a..e6e9bc2 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8 + uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 + uses: marocchino/sticky-pull-request-comment@773744901bac0e8cbb5a0dc842800d45e9b2b405 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml deleted file mode 100644 index 76a9e67..0000000 --- a/.github/workflows/release-announcements.yml +++ /dev/null @@ -1,42 +0,0 @@ -name: release-announcements -# Automatic release toot and tweet anouncements -on: - release: - types: [published] - workflow_dispatch: - -jobs: - toot: - runs-on: ubuntu-latest - steps: - - name: get topics and convert to hashtags - id: get_topics - run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - - - 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 }} - - ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics - - bsky-post: - runs-on: ubuntu-latest - steps: - - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 - with: - post: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - env: - BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} - BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} - # diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml deleted file mode 100644 index 537529b..0000000 --- a/.github/workflows/template_version_comment.yml +++ /dev/null @@ -1,46 +0,0 @@ -name: nf-core template version comment -# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. -# It posts a comment to the PR, even if it comes from a fork. - -on: pull_request_target - -jobs: - template_version: - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - with: - ref: ${{ github.event.pull_request.head.sha }} - - - name: Read template version from .nf-core.yml - uses: nichmor/minimal-read-yaml@v0.0.2 - id: read_yml - with: - config: ${{ github.workspace }}/.nf-core.yml - - - name: Install nf-core - run: | - python -m pip install --upgrade pip - pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - - name: Check nf-core outdated - id: nf_core_outdated - run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - - - name: Post nf-core template version comment - uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 - if: | - contains(env.OUTPUT, 'nf-core') - with: - repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} - allow-repeats: false - message: | - > [!WARNING] - > Newer version of the nf-core template is available. - > - > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. - > Please update your pipeline to the latest version. - > - > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). - # diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index 83599f6..0000000 --- a/.gitpod.yml +++ /dev/null @@ -1,10 +0,0 @@ -image: nfcore/gitpod:latest -tasks: - - name: Update Nextflow and setup pre-commit - command: | - pre-commit install --install-hooks - nextflow self-update - -vscode: - extensions: - - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index 7e7208c..07f5253 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,18 +1,34 @@ +lint: + actions_awsfulltest: false + actions_awstest: false + files_exist: + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml + - conf/igenomes.config + - conf/igenomes_ignored.config + files_unchanged: + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/ISSUE_TEMPLATE/feature_request.yml + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/linting.yml + - .prettierignore + - assets/sendmail_template.txt + - docs/README.md + multiqc_config: false +nf_core_version: 3.5.2 repository_type: pipeline - -nf_core_version: 3.2.1 - -lint: {} - template: - org: nf-core - name: postprocessing + author: Clinical Genomics Stockholm description: Customizable post-processing and extension layer built on top of Oncoanalyser that adapts its outputs to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser robust core - author: Clinical Genomics Stockholm - version: 1.0.0dev - force: true + force: false + is_nfcore: false + name: oncorefiner + org: Clinical-Genomics outdir: . - is_nfcore: true + skip_features: + - igenomes + - fastqc + version: 1.0.0dev diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1dec865..d06777a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,10 +4,24 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.2.5 - - - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "3.1.2" + - prettier@3.6.2 + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v6.0.0 hooks: - - id: editorconfig-checker - alias: ec + - id: trailing-whitespace + args: [--markdown-linebreak-ext=md] + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/nf-core/.*| + subworkflows/nf-core/.*| + .*\.snap$ + )$ + - id: end-of-file-fixer + exclude: | + (?x)^( + .*ro-crate-metadata.json$| + modules/nf-core/.*| + subworkflows/nf-core/.*| + .*\.snap$ + )$ diff --git a/.prettierignore b/.prettierignore index edd29f0..dd749d4 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,4 +10,7 @@ testing/ testing* *.pyc bin/ +.nf-test/ ro-crate-metadata.json +modules/nf-core/ +subworkflows/nf-core/ diff --git a/.prettierrc.yml b/.prettierrc.yml index c81f9a7..07dbd8b 100644 --- a/.prettierrc.yml +++ b/.prettierrc.yml @@ -1 +1,6 @@ printWidth: 120 +tabWidth: 4 +overrides: + - files: "*.{md,yml,yaml,html,css,scss,js,cff}" + options: + tabWidth: 2 diff --git a/CHANGELOG.md b/CHANGELOG.md index cc025cd..950294d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,11 @@ -# nf-core/postprocessing: Changelog +# Clinical-Genomics/oncorefiner: 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). ## v1.0.0dev - [date] -Initial release of nf-core/postprocessing, created with the [nf-core](https://nf-co.re/) template. +Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](https://nf-co.re/) template. ### `Added` diff --git a/CITATIONS.md b/CITATIONS.md index 2de0056..2b87728 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,4 +1,4 @@ -# nf-core/postprocessing: Citations +# Clinical-Genomics/oncorefiner: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) @@ -10,10 +10,6 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/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. diff --git a/LICENSE b/LICENSE index a6e4a41..3128835 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) The nf-core/postprocessing team +Copyright (c) The Clinical-Genomics/oncorefiner team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index e455a8e..9225cb9 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,20 @@ -

- - - nf-core/postprocessing - -

- -[![GitHub Actions CI Status](https://github.com/nf-core/postprocessing/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/postprocessing/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/postprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/postprocessing/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/postprocessing/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +# Clinical-Genomics/oncorefiner + +[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/Clinical-Genomics/oncorefiner) +[![GitHub Actions CI Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml) +[![GitHub Actions Linting Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/) +[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/postprocessing) - -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23postprocessing-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/postprocessing)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/Clinical-Genomics/oncorefiner) ## Introduction -**nf-core/postprocessing** is a bioinformatics pipeline that ... +**Clinical-Genomics/oncorefiner** is a bioinformatics pipeline that ... -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) + workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples. --> +2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage @@ -57,7 +52,7 @@ Now, you can run the pipeline using: ```bash -nextflow run nf-core/postprocessing \ +nextflow run Clinical-Genomics/oncorefiner \ -profile \ --input samplesheet.csv \ --outdir @@ -66,17 +61,9 @@ nextflow run nf-core/postprocessing \ > [!WARNING] > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). -For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/postprocessing/usage) and the [parameter documentation](https://nf-co.re/postprocessing/parameters). - -## Pipeline output - -To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/postprocessing/results) tab on the nf-core website pipeline page. -For more details about the output files and reports, please refer to the -[output documentation](https://nf-co.re/postprocessing/output). - ## Credits -nf-core/postprocessing was originally written by Clinical Genomics Stockholm. +Clinical-Genomics/oncorefiner was originally written by Clinical Genomics Stockholm. We thank the following people for their extensive assistance in the development of this pipeline: @@ -86,18 +73,16 @@ We thank the following people for their extensive assistance in the development 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 `#postprocessing` channel](https://nfcore.slack.com/channels/postprocessing) (you can join with [this invite](https://nf-co.re/join/slack)). - ## Citations - + 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: +This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE). > **The nf-core framework for community-curated bioinformatics pipelines.** > diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json index baeda08..4bb55ee 100644 --- a/assets/adaptivecard.json +++ b/assets/adaptivecard.json @@ -17,7 +17,7 @@ "size": "Large", "weight": "Bolder", "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "nf-core/postprocessing v${version} - ${runName}", + "text": "Clinical-Genomics/oncorefiner v${version} - ${runName}", "wrap": true }, { diff --git a/assets/email_template.html b/assets/email_template.html index 5f2b8de..9f30418 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,21 +4,21 @@ - - nf-core/postprocessing Pipeline Report + + Clinical-Genomics/oncorefiner Pipeline Report
-

nf-core/postprocessing ${version}

+

Clinical-Genomics/oncorefiner ${version}

Run Name: $runName

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

nf-core/postprocessing execution completed unsuccessfully!

+

Clinical-Genomics/oncorefiner execution completed unsuccessfully!

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

The full error message was:

${errorReport}
@@ -27,7 +27,7 @@

nf-core/postprocessing execution compl } else { out << """
- nf-core/postprocessing execution completed successfully! + Clinical-Genomics/oncorefiner execution completed successfully!
""" } @@ -44,8 +44,8 @@

Pipeline Configuration:

-

nf-core/postprocessing

-

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

+

Clinical-Genomics/oncorefiner

+

https://github.com/Clinical-Genomics/oncorefiner

diff --git a/assets/email_template.txt b/assets/email_template.txt index 0251adb..95ff073 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -1,18 +1,10 @@ ----------------------------------------------------- - ,--./,-. - ___ __ __ __ ___ /,-._.--~\\ - |\\ | |__ __ / ` / \\ |__) |__ } { - | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, - `._,._,' - nf-core/postprocessing ${version} ----------------------------------------------------- Run Name: $runName <% if (success){ - out << "## nf-core/postprocessing execution completed successfully! ##" + out << "## Clinical-Genomics/oncorefiner execution completed successfully! ##" } else { out << """#################################################### -## nf-core/postprocessing execution completed unsuccessfully! ## +## Clinical-Genomics/oncorefiner execution completed unsuccessfully! ## #################################################### The exit status of the task that caused the workflow execution to fail was: $exitStatus. The full error message was: @@ -35,5 +27,5 @@ Pipeline Configuration: <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> -- -nf-core/postprocessing -https://github.com/nf-core/postprocessing +Clinical-Genomics/oncorefiner +https://github.com/Clinical-Genomics/oncorefiner diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index e8f75b9..81e8771 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -1,13 +1,13 @@ -id: "nf-core-postprocessing-methods-description" +id: "Clinical-Genomics-oncorefiner-methods-description" description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "nf-core/postprocessing Methods Description" -section_href: "https://github.com/nf-core/postprocessing" +section_name: "Clinical-Genomics/oncorefiner Methods Description" +section_href: "https://github.com/Clinical-Genomics/oncorefiner" plot_type: "html" ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using nf-core/postprocessing v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

+

Data was processed using Clinical-Genomics/oncorefiner v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}

${tool_citations}

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c8841ae..38c7b0f 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,13 +1,12 @@ report_comment: > - This report has been generated by the nf-core/postprocessing - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the Clinical-Genomics/oncorefiner + analysis pipeline. report_section_order: - "nf-core-postprocessing-methods-description": + "Clinical-Genomics-oncorefiner-methods-description": order: -1000 software_versions: order: -1001 - "nf-core-postprocessing-summary": + "Clinical-Genomics-oncorefiner-summary": order: -1002 export_plots: true diff --git a/assets/nf-core-oncorefiner_logo_light.png b/assets/nf-core-oncorefiner_logo_light.png new file mode 100644 index 0000000..8265259 Binary files /dev/null and b/assets/nf-core-oncorefiner_logo_light.png differ diff --git a/assets/nf-core-postprocessing_logo_light.png b/assets/nf-core-postprocessing_logo_light.png deleted file mode 100644 index a01e3fa..0000000 Binary files a/assets/nf-core-postprocessing_logo_light.png and /dev/null differ diff --git a/assets/schema_input.json b/assets/schema_input.json index 0624638..64700a3 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/postprocessing/master/assets/schema_input.json", - "title": "nf-core/postprocessing pipeline - params.input schema", + "$id": "https://raw.githubusercontent.com/Clinical-Genomics/oncorefiner/master/assets/schema_input.json", + "title": "Clinical-Genomics/oncorefiner pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", "items": { @@ -17,14 +17,14 @@ "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt index abc62e5..1a1595f 100644 --- a/assets/sendmail_template.txt +++ b/assets/sendmail_template.txt @@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8 $email_html --nfcoremimeboundary -Content-Type: image/png;name="nf-core-postprocessing_logo.png" +Content-Type: image/png;name="Clinical-Genomics-oncorefiner_logo.png" Content-Transfer-Encoding: base64 Content-ID: -Content-Disposition: inline; filename="nf-core-postprocessing_logo_light.png" +Content-Disposition: inline; filename="Clinical-Genomics-oncorefiner_logo_light.png" -<% out << new File("$projectDir/assets/nf-core-postprocessing_logo_light.png"). +<% out << new File("$projectDir/assets/Clinical-Genomics-oncorefiner_logo_light.png"). bytes. encodeBase64(). toString(). diff --git a/assets/slackreport.json b/assets/slackreport.json index 6ac5469..445f65a 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/postprocessing ${version} - ${runName}", + "author_name": "Clinical-Genomics/oncorefiner ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/base.config b/conf/base.config index 520e574..3c71de9 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - nf-core/postprocessing Nextflow base config file + Clinical-Genomics/oncorefiner Nextflow base config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A 'blank slate' config file, appropriate for general use on most high performance compute environments. Assumes that all software is installed and available on @@ -15,7 +15,7 @@ process { memory = { 6.GB * task.attempt } time = { 4.h * task.attempt } - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' @@ -59,4 +59,8 @@ process { errorStrategy = 'retry' maxRetries = 2 } + withLabel: process_gpu { + ext.use_gpu = { workflow.profile.contains('gpu') } + accelerator = { workflow.profile.contains('gpu') ? 1 : null } + } } diff --git a/conf/igenomes.config b/conf/igenomes.config deleted file mode 100644 index 3f11437..0000000 --- a/conf/igenomes.config +++ /dev/null @@ -1,440 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines reference genomes using iGenome paths. - Can be used by any config that customises the base path using: - $params.igenomes_base / --igenomes_base ----------------------------------------------------------------------------------------- -*/ - -params { - // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } -} diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config deleted file mode 100644 index b4034d8..0000000 --- a/conf/igenomes_ignored.config +++ /dev/null @@ -1,9 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Empty genomes dictionary to use when igenomes is ignored. ----------------------------------------------------------------------------------------- -*/ - -params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index d203d2b..f0b0d55 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,10 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: FASTQC { - ext.args = '--quiet' - } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index 75f64a5..aa5c8ea 100644 --- a/conf/test.config +++ b/conf/test.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/postprocessing -profile test, --outdir + nextflow run Clinical-Genomics/oncorefiner -profile test, --outdir ---------------------------------------------------------------------------------------- */ @@ -25,6 +25,5 @@ params { // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references - genome = 'R64-1-1' + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' } diff --git a/conf/test_full.config b/conf/test_full.config index 8a56b82..47a14b7 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/postprocessing -profile test_full, --outdir + nextflow run Clinical-Genomics/oncorefiner -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ @@ -19,6 +19,6 @@ params { // TODO nf-core: Give any required params for the test so that command line flags are not needed input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' - // Genome references - genome = 'R64-1-1' + // Fasta references + fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz' } diff --git a/docs/README.md b/docs/README.md index f6ed5c2..eac0051 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,10 +1,8 @@ -# nf-core/postprocessing: Documentation +# Clinical-Genomics/oncorefiner: Documentation -The nf-core/postprocessing documentation is split into the following pages: +The Clinical-Genomics/oncorefiner documentation is split into the following pages: - [Usage](usage.md) - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. - [Output](output.md) - An overview of the different results produced by the pipeline and how to interpret them. - -You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re) diff --git a/docs/images/nf-core-oncorefiner_logo_dark.png b/docs/images/nf-core-oncorefiner_logo_dark.png new file mode 100644 index 0000000..3b69dc0 Binary files /dev/null and b/docs/images/nf-core-oncorefiner_logo_dark.png differ diff --git a/docs/images/nf-core-oncorefiner_logo_light.png b/docs/images/nf-core-oncorefiner_logo_light.png new file mode 100644 index 0000000..75e5a3c Binary files /dev/null and b/docs/images/nf-core-oncorefiner_logo_light.png differ diff --git a/docs/images/nf-core-postprocessing_logo_dark.png b/docs/images/nf-core-postprocessing_logo_dark.png deleted file mode 100644 index 44a16d9..0000000 Binary files a/docs/images/nf-core-postprocessing_logo_dark.png and /dev/null differ diff --git a/docs/images/nf-core-postprocessing_logo_light.png b/docs/images/nf-core-postprocessing_logo_light.png deleted file mode 100644 index 9f7ad03..0000000 Binary files a/docs/images/nf-core-postprocessing_logo_light.png and /dev/null differ diff --git a/docs/output.md b/docs/output.md index 8b773d5..2447844 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,4 +1,4 @@ -# nf-core/postprocessing: Output +# Clinical-Genomics/oncorefiner: Output ## Introduction @@ -12,23 +12,9 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution -### FastQC - -
-Output files - -- `fastqc/` - - `*_fastqc.html`: FastQC report containing quality metrics. - - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. - -
- -[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). - ### MultiQC
diff --git a/docs/usage.md b/docs/usage.md index 1345c8f..4e866cb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,6 +1,4 @@ -# nf-core/postprocessing: Usage - -## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/postprocessing/usage](https://nf-co.re/postprocessing/usage) +# Clinical-Genomics/oncorefiner: Usage > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ @@ -57,7 +55,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/postprocessing --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run Clinical-Genomics/oncorefiner --input ./samplesheet.csv --outdir ./results -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -81,7 +79,7 @@ Pipeline settings can be provided in a `yaml` or `json` file via `-params-file < The above pipeline run specified with a params file in yaml format: ```bash -nextflow run nf-core/postprocessing -profile docker -params-file params.yaml +nextflow run Clinical-Genomics/oncorefiner -profile docker -params-file params.yaml ``` with: @@ -89,7 +87,6 @@ with: ```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' -genome: 'GRCh37' <...> ``` @@ -100,14 +97,14 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: ```bash -nextflow pull nf-core/postprocessing +nextflow pull Clinical-Genomics/oncorefiner ``` ### Reproducibility It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [nf-core/postprocessing releases page](https://github.com/nf-core/postprocessing/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. +First, go to the [Clinical-Genomics/oncorefiner releases page](https://github.com/Clinical-Genomics/oncorefiner/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. @@ -149,7 +146,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `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/) + - A generic configuration profile to be used with [Charliecloud](https://charliecloud.io/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `wave` diff --git a/main.nf b/main.nf index e4904fd..dedafb2 100644 --- a/main.nf +++ b/main.nf @@ -1,11 +1,9 @@ #!/usr/bin/env nextflow /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - nf-core/postprocessing + Clinical-Genomics/oncorefiner ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Github : https://github.com/nf-core/postprocessing - Website: https://nf-co.re/postprocessing - Slack : https://nfcore.slack.com/channels/postprocessing + Github : https://github.com/Clinical-Genomics/oncorefiner ---------------------------------------------------------------------------------------- */ @@ -15,22 +13,9 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { POSTPROCESSING } from './workflows/postprocessing' -include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_postprocessing_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_postprocessing_pipeline' -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_postprocessing_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` -params.fasta = getGenomeAttribute('fasta') - +include { ONCOREFINER } from './workflows/oncorefiner' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_oncorefiner_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_oncorefiner_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -40,7 +25,7 @@ params.fasta = getGenomeAttribute('fasta') // // WORKFLOW: Run main analysis pipeline depending on type of input // -workflow NFCORE_POSTPROCESSING { +workflow CLINICALGENOMICS_ONCOREFINER { take: samplesheet // channel: samplesheet read in from --input @@ -50,11 +35,11 @@ workflow NFCORE_POSTPROCESSING { // // WORKFLOW: Run pipeline // - POSTPROCESSING ( + ONCOREFINER ( samplesheet ) emit: - multiqc_report = POSTPROCESSING.out.multiqc_report // channel: /path/to/multiqc_report.html + multiqc_report = ONCOREFINER.out.multiqc_report // channel: /path/to/multiqc_report.html } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -74,13 +59,16 @@ workflow { params.monochrome_logs, args, params.outdir, - params.input + params.input, + params.help, + params.help_full, + params.show_hidden ) // // WORKFLOW: Run main workflow // - NFCORE_POSTPROCESSING ( + CLINICALGENOMICS_ONCOREFINER ( PIPELINE_INITIALISATION.out.samplesheet ) // @@ -93,7 +81,7 @@ workflow { params.outdir, params.monochrome_logs, params.hook_url, - NFCORE_POSTPROCESSING.out.multiqc_report + CLINICALGENOMICS_ONCOREFINER.out.multiqc_report ) } diff --git a/modules.json b/modules.json index cbca3e8..dfe53ca 100644 --- a/modules.json +++ b/modules.json @@ -1,18 +1,13 @@ { - "name": "nf-core/postprocessing", - "homePage": "https://github.com/nf-core/postprocessing", + "name": "Clinical-Genomics/oncorefiner", + "homePage": "https://github.com/Clinical-Genomics/oncorefiner", "repos": { "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "fastqc": { - "branch": "master", - "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", - "installed_by": ["modules"] - }, "multiqc": { "branch": "master", - "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", + "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49", "installed_by": ["modules"] } } @@ -21,17 +16,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", + "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", + "git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml deleted file mode 100644 index 691d4c7..0000000 --- a/modules/nf-core/fastqc/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index 033f415..0000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,64 +0,0 @@ -process FASTQC { - tag "${meta.id}" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : - 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ') - - // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) - // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 - // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null - // FastQC memory value allowed range (100 - 10000) - def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) - - """ - printf "%s %s\\n" ${rename_to} | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - ${args} \\ - --threads ${task.cpus} \\ - --memory ${fastqc_memory} \\ - ${renamed_files} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index 2b2e62b..0000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,67 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] - identifier: biotools:fastqc -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. -output: - - html: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.zip": - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index e9d79a0..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,309 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - 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 }, - // 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[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } - ) - } - } - - 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("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } - ) - } - } - - 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("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } - ) - } - } - - 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("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } - ) - } - } - - 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("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } - ) - } - } - - 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("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } - ) - } - } - - 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).match() } - ) - } - } - - test("sarscov2 paired-end [fastq] - stub") { - - options "-stub" - 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 snapshot(process.out).match() } - ) - } - } - - test("sarscov2 interleaved [fastq] - stub") { - - options "-stub" - 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 snapshot(process.out).match() } - ) - } - } - - test("sarscov2 paired-end [bam] - stub") { - - options "-stub" - 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 snapshot(process.out).match() } - ) - } - } - - test("sarscov2 multiple [fastq] - stub") { - - options "-stub" - 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 snapshot(process.out).match() } - ) - } - } - - test("sarscov2 custom_prefix - stub") { - - options "-stub" - 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 snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap deleted file mode 100644 index d5db309..0000000 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ /dev/null @@ -1,392 +0,0 @@ -{ - "sarscov2 custom_prefix": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:16.374038" - }, - "sarscov2 single-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:24.993809" - }, - "sarscov2 custom_prefix - stub": { - "content": [ - { - "0": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:03:10.93942" - }, - "sarscov2 interleaved [fastq]": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:42.355718" - }, - "sarscov2 paired-end [bam]": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:53.276274" - }, - "sarscov2 multiple [fastq]": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:05.527626" - }, - "sarscov2 paired-end [fastq]": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:31.188871" - }, - "sarscov2 paired-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:34.273566" - }, - "sarscov2 multiple [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:03:02.304411" - }, - "sarscov2 single-end [fastq]": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:19.095607" - }, - "sarscov2 interleaved [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:44.640184" - }, - "sarscov2 paired-end [bam] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:53.550742" - } -} \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a27122c..d02016a 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.27 + - bioconda::multiqc=1.32 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 58d9313..c1158fb 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : - 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' : + 'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index b16c187..ce30eb7 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -15,57 +15,71 @@ tools: licence: ["GPL-3.0-or-later"] identifier: biotools:multiqc 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: + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + ontologies: [] + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + ontologies: [] + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV +output: + report: + - "*multiqc_report.html": type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - - replace_names: + description: MultiQC report file + pattern: "multiqc_report.html" + ontologies: [] + data: + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - "*_plots": type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - - sample_names: + description: Plots created by MultiQC + pattern: "*_data" + ontologies: [] + versions: + - versions.yml: type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" -output: - - report: - - "*multiqc_report.html": - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - - "*_plots": - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7b7c132..a88bafd 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.3", "nextflow": "24.10.4" }, - "timestamp": "2025-01-27T09:29:57.631982377" + "timestamp": "2025-10-27T13:33:24.356715" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.3", "nextflow": "24.10.4" }, - "timestamp": "2025-01-27T09:30:34.743726958" + "timestamp": "2025-10-27T13:34:11.103619" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f" ] ], "meta": { - "nf-test": "0.9.2", + "nf-test": "0.9.3", "nextflow": "24.10.4" }, - "timestamp": "2025-01-27T09:30:21.44383553" + "timestamp": "2025-10-27T13:34:04.615233" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d..0000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index e0d3116..a707fa7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - nf-core/postprocessing Nextflow config file + Clinical-Genomics/oncorefiner Nextflow config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- @@ -13,11 +13,6 @@ params { // Input options input = null - // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes/' - igenomes_ignore = false - // MultiQC options multiqc_config = null multiqc_title = null @@ -32,13 +27,15 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false - hook_url = null + hook_url = System.getenv('HOOK_URL') help = false help_full = false show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + + // Config options config_profile_name = null config_profile_description = null @@ -91,7 +88,18 @@ profiles { apptainer.enabled = false docker.runOptions = '-u $(id -u):$(id -g)' } - arm { + arm64 { + process.arch = 'arm64' + // TODO https://github.com/nf-core/modules/issues/6694 + // For now if you're using arm64 you have to use wave for the sake of the maintainers + // wave profile + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' + } + emulate_amd64 { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { @@ -148,28 +156,25 @@ profiles { wave.freeze = true wave.strategy = 'conda,container' } - gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB - process { - resourceLimits = [ - memory: 8.GB, - cpus : 4, - time : 1.h - ] - } + gpu { + docker.runOptions = '-u $(id -u):$(id -g) --gpus all' + apptainer.runOptions = '--nv' + singularity.runOptions = '--nv' } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } -// Load nf-core custom profiles from different Institutions -includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" +// Load nf-core custom profiles from different institutions + +// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. +// Load Clinical-Genomics/oncorefiner custom profiles from different institutions. +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Load nf-core/postprocessing custom profiles from different institutions. + +// Load Clinical-Genomics/oncorefiner custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/postprocessing.config" : "/dev/null" +// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/oncorefiner.config" : "/dev/null" // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled @@ -180,8 +185,7 @@ podman.registry = 'quay.io' singularity.registry = 'quay.io' charliecloud.registry = 'quay.io' -// Load igenomes.config if required -includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // 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. @@ -225,8 +229,7 @@ dag { } manifest { - name = 'nf-core/postprocessing' - author = """Clinical Genomics Stockholm""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead + name = 'Clinical-Genomics/oncorefiner' contributors = [ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ @@ -238,50 +241,23 @@ manifest { orcid: '' ], ] - homePage = 'https://github.com/nf-core/postprocessing' + homePage = 'https://github.com/Clinical-Genomics/oncorefiner' description = """Customizable post-processing and extension layer built on top of Oncoanalyser that adapts its outputs to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser robust core""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=24.04.2' + nextflowVersion = '!>=25.04.0' version = '1.0.0dev' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { defaultIgnoreParams = ["genomes"] monochromeLogs = params.monochrome_logs - help { - enabled = true - command = "nextflow run nf-core/postprocessing -profile --input samplesheet.csv --outdir " - fullParameter = "help_full" - showHiddenParameter = "show_hidden" - beforeText = """ --\033[2m----------------------------------------------------\033[0m- - \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m -\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m -\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m -\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m - \033[0;32m`._,._,\'\033[0m -\033[0;35m nf-core/postprocessing ${manifest.version}\033[0m --\033[2m----------------------------------------------------\033[0m- -""" - afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} -* The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x - -* Software dependencies - https://github.com/nf-core/postprocessing/blob/master/CITATIONS.md -""" - } - summary { - beforeText = validation.help.beforeText - afterText = validation.help.afterText - } } // Load modules.config for DSL2 module specific options diff --git a/nextflow_schema.json b/nextflow_schema.json index 0f31df0..5c5d2f4 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/postprocessing/master/nextflow_schema.json", - "title": "nf-core/postprocessing pipeline parameters", + "$id": "https://raw.githubusercontent.com/Clinical-Genomics/oncorefiner/master/nextflow_schema.json", + "title": "Clinical-Genomics/oncorefiner pipeline parameters", "description": "Customizable post-processing and extension layer built on top of Oncoanalyser that adapts its outputs to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser robust core", "type": "object", "$defs": { @@ -20,7 +20,7 @@ "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", "description": "Path to comma-separated file containing information about the samples in the experiment.", - "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/postprocessing/usage#samplesheet-input).", + "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.", "fa_icon": "fas fa-file-csv" }, "outdir": { @@ -43,45 +43,6 @@ } } }, - "reference_genome_options": { - "title": "Reference genome options", - "type": "object", - "fa_icon": "fas fa-dna", - "description": "Reference genome related files and options required for the workflow.", - "properties": { - "genome": { - "type": "string", - "description": "Name of iGenomes reference.", - "fa_icon": "fas fa-book", - "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." - }, - "fasta": { - "type": "string", - "format": "file-path", - "exists": true, - "mimetype": "text/plain", - "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", - "description": "Path to FASTA genome file.", - "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", - "fa_icon": "far fa-file-code" - }, - "igenomes_ignore": { - "type": "boolean", - "description": "Do not load the iGenomes reference config.", - "fa_icon": "fas fa-ban", - "hidden": true, - "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." - }, - "igenomes_base": { - "type": "string", - "format": "directory-path", - "description": "The base path to the igenomes reference files", - "fa_icon": "fas fa-ban", - "hidden": true, - "default": "s3://ngi-igenomes/igenomes/" - } - } - }, "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -224,6 +185,18 @@ "fa_icon": "far calendar", "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", "hidden": true + }, + "help": { + "type": ["boolean", "string"], + "description": "Display the help message." + }, + "help_full": { + "type": "boolean", + "description": "Display the full detailed help message." + }, + "show_hidden": { + "type": "boolean", + "description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)." } } } @@ -232,9 +205,6 @@ { "$ref": "#/$defs/input_output_options" }, - { - "$ref": "#/$defs/reference_genome_options" - }, { "$ref": "#/$defs/institutional_config_options" }, diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 0c32efa..b0a1bdf 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-10-02T08:07:59+00:00", - "description": "

\n \n \n \"nf-core/postprocessing\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/postprocessing/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/postprocessing/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/postprocessing/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/postprocessing/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/postprocessing/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/postprocessing)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23postprocessing-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/postprocessing)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/postprocessing** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/postprocessing \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/postprocessing/usage) and the [parameter documentation](https://nf-co.re/postprocessing/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/postprocessing/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/postprocessing/output).\n\n## Credits\n\nnf-core/postprocessing was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#postprocessing` channel](https://nfcore.slack.com/channels/postprocessing) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2026-03-10T09:35:17+00:00", + "description": "# Clinical-Genomics/oncorefiner\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/Clinical-Genomics/oncorefiner)\n[![GitHub Actions CI Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/Clinical-Genomics/oncorefiner)\n\n## Introduction\n\n**Clinical-Genomics/oncorefiner** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run Clinical-Genomics/oncorefiner \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Credits\n\nClinical-Genomics/oncorefiner was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -37,9 +37,6 @@ { "@id": "docs/" }, - { - "@id": "docs/images/" - }, { "@id": "modules/" }, @@ -67,9 +64,6 @@ { "@id": "LICENSE" }, - { - "@id": "CODE_OF_CONDUCT.md" - }, { "@id": "CITATIONS.md" }, @@ -92,17 +86,17 @@ "@id": ".prettierignore" } ], - "isBasedOn": "https://github.com/nf-core/postprocessing", + "isBasedOn": "https://github.com/Clinical-Genomics/oncorefiner", "license": "MIT", "mainEntity": { "@id": "main.nf" }, "mentions": [ { - "@id": "#a56bc4c4-6ec5-4306-acd0-eddfedb4c6b9" + "@id": "#840a852b-c00b-4c7e-8f78-e7f16cead854" } ], - "name": "nf-core/postprocessing" + "name": "Clinical-Genomics/oncorefiner" }, { "@id": "ro-crate-metadata.json", @@ -126,8 +120,13 @@ "SoftwareSourceCode", "ComputationalWorkflow" ], + "creator": [ + { + "@id": "#eva.caceres@scilifelab.se" + } + ], "dateCreated": "", - "dateModified": "2025-10-02T10:07:59Z", + "dateModified": "2026-03-10T10:35:17Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -137,7 +136,7 @@ "MIT" ], "name": [ - "nf-core/postprocessing" + "Clinical-Genomics/oncorefiner" ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" @@ -146,8 +145,8 @@ "@id": "https://nf-co.re/" }, "url": [ - "https://github.com/nf-core/postprocessing", - "https://nf-co.re/postprocessing/dev/" + "https://github.com/Clinical-Genomics/oncorefiner", + "https://nf-co.re/Clinical-Genomics/oncorefiner/dev/" ], "version": [ "1.0.0dev" @@ -163,26 +162,26 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=24.04.2" + "version": "!>=25.04.0" }, { - "@id": "#a56bc4c4-6ec5-4306-acd0-eddfedb4c6b9", + "@id": "#840a852b-c00b-4c7e-8f78-e7f16cead854", "@type": "TestSuite", "instance": [ { - "@id": "#0ce223c5-8270-496b-9e30-86656563e505" + "@id": "#4a7f909b-3ca2-43d7-8e04-dd68097d4b8d" } ], "mainEntity": { "@id": "main.nf" }, - "name": "Test suite for nf-core/postprocessing" + "name": "Test suite for Clinical-Genomics/oncorefiner" }, { - "@id": "#0ce223c5-8270-496b-9e30-86656563e505", + "@id": "#4a7f909b-3ca2-43d7-8e04-dd68097d4b8d", "@type": "TestInstance", - "name": "GitHub Actions workflow for testing nf-core/postprocessing", - "resource": "repos/nf-core/postprocessing/actions/workflows/ci.yml", + "name": "GitHub Actions workflow for testing Clinical-Genomics/oncorefiner", + "resource": "repos/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml", "runsOn": { "@id": "https://w3id.org/ro/terms/test#GithubService" }, @@ -211,11 +210,6 @@ "@type": "Dataset", "description": "Markdown files for documenting the pipeline" }, - { - "@id": "docs/images/", - "@type": "Dataset", - "description": "Images for the documentation files" - }, { "@id": "modules/", "@type": "Dataset", @@ -261,11 +255,6 @@ "@type": "File", "description": "The license - should be MIT" }, - { - "@id": "CODE_OF_CONDUCT.md", - "@type": "File", - "description": "The nf-core code of conduct" - }, { "@id": "CITATIONS.md", "@type": "File", @@ -306,6 +295,12 @@ "@type": "Organization", "name": "nf-core", "url": "https://nf-co.re/" + }, + { + "@id": "#eva.caceres@scilifelab.se", + "@type": "Person", + "email": "eva.caceres@scilifelab.se", + "name": "Eva Caceres" } ] } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_postprocessing_pipeline/main.nf b/subworkflows/local/utils_nfcore_postprocessing_pipeline/main.nf deleted file mode 100644 index f487f3b..0000000 --- a/subworkflows/local/utils_nfcore_postprocessing_pipeline/main.nf +++ /dev/null @@ -1,264 +0,0 @@ -// -// Subworkflow with functionality specific to the nf-core/postprocessing pipeline -// - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { samplesheetToList } from 'plugin/nf-schema' -include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' -include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { imNotification } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - SUBWORKFLOW TO INITIALISE PIPELINE -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow PIPELINE_INITIALISATION { - - take: - version // boolean: Display version and exit - validate_params // boolean: Boolean whether to validate parameters against the schema at runtime - monochrome_logs // boolean: Do not use coloured log outputs - nextflow_cli_args // array: List of positional nextflow CLI args - outdir // string: The output directory where the results will be saved - input // string: Path to input samplesheet - - main: - - ch_versions = Channel.empty() - - // - // Print version and exit if required and dump pipeline parameters to JSON file - // - UTILS_NEXTFLOW_PIPELINE ( - version, - true, - outdir, - workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 - ) - - // - // Validate parameters and generate parameter summary to stdout - // - UTILS_NFSCHEMA_PLUGIN ( - workflow, - validate_params, - null - ) - - // - // Check config provided to the pipeline - // - UTILS_NFCORE_PIPELINE ( - nextflow_cli_args - ) - - // - // Custom validation for pipeline parameters - // - validateInputParameters() - - // - // Create channel from input file provided through params.input - // - - Channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() - .map { samplesheet -> - validateInputSamplesheet(samplesheet) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } - .set { ch_samplesheet } - - emit: - samplesheet = ch_samplesheet - versions = ch_versions -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - SUBWORKFLOW FOR PIPELINE COMPLETION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow PIPELINE_COMPLETION { - - take: - email // string: email address - email_on_fail // string: email address sent on pipeline failure - plaintext_email // boolean: Send plain-text email instead of HTML - outdir // path: Path to output directory where results will be published - monochrome_logs // boolean: Disable ANSI colour codes in log output - hook_url // string: hook URL for notifications - multiqc_report // string: Path to MultiQC report - - main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - def multiqc_reports = multiqc_report.toList() - - // - // Completion email and summary - // - workflow.onComplete { - if (email || email_on_fail) { - completionEmail( - summary_params, - email, - email_on_fail, - plaintext_email, - outdir, - monochrome_logs, - multiqc_reports.getVal(), - ) - } - - completionSummary(monochrome_logs) - if (hook_url) { - imNotification(summary_params, hook_url) - } - } - - workflow.onError { - log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" - } -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ -// -// Check and validate pipeline parameters -// -def validateInputParameters() { - genomeExistsError() -} - -// -// Validate channels from input samplesheet -// -def validateInputSamplesheet(input) { - def (metas, fastqs) = input[1..2] - - // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 - if (!endedness_ok) { - error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") - } - - return [ metas[0], fastqs ] -} -// -// Get attribute from genome config file e.g. fasta -// -def getGenomeAttribute(attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null -} - -// -// Exit pipeline if incorrect --genome key provided -// -def genomeExistsError() { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - error(error_string) - } -} -// -// Generate methods description for MultiQC -// -def toolCitationText() { - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def citation_text = [ - "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text -} - -def toolBibliographyText() { - // TODO nf-core: Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " - ].join(' ').trim() - - return reference_text -} - -def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = workflow.toMap() - meta["manifest_map"] = workflow.manifest.toMap() - - // Pipeline DOI - if (meta.manifest_map.doi) { - // Using a loop to handle multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - def temp_doi_ref = "" - def manifest_doi = meta.manifest_map.doi.tokenize(",") - manifest_doi.each { doi_ref -> - temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " - } - meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) - } else meta["doi_text"] = "" - meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - // meta["tool_bibliography"] = toolBibliographyText() - - - def methods_text = mqc_methods_yaml.text - - def engine = new groovy.text.SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html.toString() -} - diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100644 index f847611..0000000 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index bfd2587..2f30e9a 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -98,7 +98,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML())) } // diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100644 index ac8523c..0000000 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf index 4994303..ee4738c 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -4,6 +4,7 @@ include { paramsSummaryLog } from 'plugin/nf-schema' include { validateParameters } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' workflow UTILS_NFSCHEMA_PLUGIN { @@ -15,29 +16,56 @@ workflow UTILS_NFSCHEMA_PLUGIN { // when this input is empty it will automatically use the configured schema or // "${projectDir}/nextflow_schema.json" as default. This input should not be empty // for meta pipelines + help // boolean: show help message + help_full // boolean: show full help message + show_hidden // boolean: show hidden parameters in help message + before_text // string: text to show before the help message and parameters summary + after_text // string: text to show after the help message and parameters summary + command // string: an example command of the pipeline main: + if(help || help_full) { + help_options = [ + beforeText: before_text, + afterText: after_text, + command: command, + showHidden: show_hidden, + fullHelp: help_full, + ] + if(parameters_schema) { + help_options << [parametersSchema: parameters_schema] + } + log.info paramsHelp( + help_options, + params.help instanceof String ? params.help : "", + ) + exit 0 + } + // // Print parameter summary to stdout. This will display the parameters // that differ from the default given in the JSON schema // + + summary_options = [:] if(parameters_schema) { - log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) - } else { - log.info paramsSummaryLog(input_workflow) + summary_options << [parametersSchema: parameters_schema] } + log.info before_text + log.info paramsSummaryLog(summary_options, input_workflow) + log.info after_text // // Validate the parameters using nextflow_schema.json or the schema // given via the validation.parametersSchema configuration option // if(validate_params) { + validateOptions = [:] if(parameters_schema) { - validateParameters(parameters_schema:parameters_schema) - } else { - validateParameters() + validateOptions << [parametersSchema: parameters_schema] } + validateParameters(validateOptions) } emit: diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 8fb3016..c977917 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -25,6 +25,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -51,6 +57,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -77,6 +89,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -103,6 +121,12 @@ nextflow_workflow { input[0] = workflow input[1] = validate_params input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = false + input[4] = false + input[5] = false + input[6] = "" + input[7] = "" + input[8] = "" """ } } @@ -114,4 +138,36 @@ nextflow_workflow { ) } } + + test("Should create a help message") { + + when { + + params { + test_data = '' + outdir = null + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + input[3] = true + input[4] = false + input[5] = false + input[6] = "Before" + input[7] = "After" + input[8] = "nextflow run test/test" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 0907ac5..8d8c737 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,8 +1,8 @@ plugins { - id "nf-schema@2.1.0" + id "nf-schema@2.5.1" } validation { parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" monochromeLogs = true -} \ No newline at end of file +} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 0000000..8f7b4a5 --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,33 @@ +{ + "-profile test": { + "content": [ + { + "Workflow": { + "Clinical-Genomics/oncorefiner": "v1.0.0dev" + } + }, + [ + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/llms-full.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc.parquet", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/oncorefiner_software_mqc_versions.yml" + ], + [ + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" + ] + ], + "meta": { + "nf-test": "0.9.3", + "nextflow": "25.10.4" + }, + "timestamp": "2026-03-10T14:07:44.258578" + } +} \ No newline at end of file diff --git a/workflows/postprocessing.nf b/workflows/postprocessing.nf deleted file mode 100644 index 8c34b33..0000000 --- a/workflows/postprocessing.nf +++ /dev/null @@ -1,97 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_postprocessing_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN MAIN WORKFLOW -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow POSTPROCESSING { - - take: - ch_samplesheet // channel: samplesheet read in from --input - main: - - ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() - // - // MODULE: Run FastQC - // - FASTQC ( - ch_samplesheet - ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - - // - // Collate and save software versions - // - softwareVersionsToYAML(ch_versions) - .collectFile( - storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_' + 'postprocessing_software_' + 'mqc_' + 'versions.yml', - sort: true, - newLine: true - ).set { ch_collated_versions } - - - // - // MODULE: MultiQC - // - ch_multiqc_config = Channel.fromPath( - "$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() - - summary_params = paramsSummaryMap( - workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? - file(params.multiqc_methods_description, checkIfExists: true) : - file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value( - methodsDescriptionText(ch_multiqc_custom_methods_description)) - - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix( - ch_methods_description.collectFile( - name: 'methods_description_mqc.yaml', - sort: true - ) - ) - - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList(), - [], - [] - ) - - emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html - versions = ch_versions // channel: [ path(versions.yml) ] - -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - THE END -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/