From 8a87f3fbdeac08a321c36d063e37c1826d7187b8 Mon Sep 17 00:00:00 2001 From: Jim Downie Date: Wed, 27 Nov 2024 10:31:25 +0000 Subject: [PATCH 1/3] Update template YML --- .nf-core.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 0894f4b..f5a803a 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -93,10 +93,8 @@ template: org: sanger-tol outdir: . skip_features: - - github - igenomes - github_badges - - nf_core_configs - codespaces - fastqc - email From 7529ee61be09c8e9e20f64b16a7fda67794390ba Mon Sep 17 00:00:00 2001 From: Jim Downie Date: Wed, 27 Nov 2024 10:31:34 +0000 Subject: [PATCH 2/3] Template update for nf-core/tools version 3.0.2 --- .gitattributes | 4 + .github/.dockstore.yml | 6 + .github/CONTRIBUTING.md | 103 +++++++++++ .github/ISSUE_TEMPLATE/bug_report.yml | 42 +++++ .github/ISSUE_TEMPLATE/feature_request.yml | 11 ++ .github/PULL_REQUEST_TEMPLATE.md | 25 +++ .github/workflows/branch.yml | 44 +++++ .github/workflows/ci.yml | 85 +++++++++ .github/workflows/clean-up.yml | 24 +++ .github/workflows/download_pipeline.yml | 119 ++++++++++++ .github/workflows/fix-linting.yml | 89 +++++++++ .github/workflows/linting.yml | 83 +++++++++ .github/workflows/linting_comment.yml | 28 +++ .../workflows/template_version_comment.yml | 46 +++++ .nf-core.yml | 170 +++++++++--------- CITATIONS.md | 2 - README.md | 3 - docs/output.md | 3 - docs/usage.md | 12 ++ nextflow.config | 14 +- nextflow_schema.json | 54 +++++- 21 files changed, 870 insertions(+), 97 deletions(-) create mode 100644 .gitattributes create mode 100644 .github/.dockstore.yml create mode 100644 .github/CONTRIBUTING.md create mode 100644 .github/ISSUE_TEMPLATE/bug_report.yml create mode 100644 .github/ISSUE_TEMPLATE/feature_request.yml create mode 100644 .github/PULL_REQUEST_TEMPLATE.md create mode 100644 .github/workflows/branch.yml create mode 100644 .github/workflows/ci.yml create mode 100644 .github/workflows/clean-up.yml create mode 100644 .github/workflows/download_pipeline.yml create mode 100644 .github/workflows/fix-linting.yml create mode 100644 .github/workflows/linting.yml create mode 100644 .github/workflows/linting_comment.yml create mode 100644 .github/workflows/template_version_comment.yml diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..7a2dabc --- /dev/null +++ b/.gitattributes @@ -0,0 +1,4 @@ +*.config linguist-language=nextflow +*.nf.test linguist-language=nextflow +modules/nf-core/** linguist-generated +subworkflows/nf-core/** linguist-generated diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml new file mode 100644 index 0000000..191fabd --- /dev/null +++ b/.github/.dockstore.yml @@ -0,0 +1,6 @@ +# Dockstore config version, not pipeline version +version: 1.2 +workflows: + - subclass: nfl + primaryDescriptorPath: /nextflow.config + publish: True diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 0000000..94f73c1 --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,103 @@ +# sanger-tol/longreadmag: Contributing Guidelines + +Hi there! +Many thanks for taking an interest in improving sanger-tol/longreadmag. + +We try to manage the required tasks for sanger-tol/longreadmag 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 ;) + +## Contribution workflow + +If you'd like to write some code for sanger-tol/longreadmag, the standard workflow is as follows: + +1. Check that there isn't already an issue about your idea in the [sanger-tol/longreadmag issues](https://github.com/sanger-tol/longreadmag/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 [sanger-tol/longreadmag repository](https://github.com/sanger-tol/longreadmag) 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 + +If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). + +## Tests + +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: + +```bash +nf-test test --profile debug,test,docker --verbose +``` + +When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. +Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. + +There are typically two types of tests that run: + +### Lint tests + +`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. + +If any failures or warnings are encountered, please follow the listed URL for more documentation. + +### Pipeline tests + +Each `nf-core` pipeline should be set up with a minimal set of test-data. +`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. +If there are any failures then the automated tests fail. +These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. + +## Patch + +:warning: Only in the unlikely and regretful event of a release happening with a bug. + +- On your own fork, make a new branch `patch` based on `upstream/master`. +- Fix the bug, and bump version (X.Y.Z+1). +- A PR should be made on `master` from patch to directly this particular bug. + +## Pipeline contribution conventions + +To make the sanger-tol/longreadmag code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. + +### Adding a new step + +If you wish to contribute a new step, please use the following coding standards: + +1. Define the corresponding input channel into your new process from the expected previous process channel +2. Write the process block (see below). +3. Define the output channel if needed (see below). +4. Add any new parameters to `nextflow.config` with a default (see below). +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`. +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`. + +### Default values + +Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. + +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. + +### Default processes resource requirements + +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. + +The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. + +### Naming schemes + +Please use the following naming schemes, to make it easy to understand what is going where. + +- initial process channel: `ch_output_from_` +- intermediate and terminal channels: `ch__for_` + +### Nextflow version bumping + +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` + +### Images and figures + +For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml new file mode 100644 index 0000000..9fcc3fc --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -0,0 +1,42 @@ +name: Bug report +description: Report something that is broken or incorrect +labels: bug +body: + - type: textarea + id: description + attributes: + label: Description of the bug + description: A clear and concise description of what the bug is. + validations: + required: true + + - type: textarea + id: command_used + attributes: + label: Command used and terminal output + description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal. + render: console + placeholder: | + $ nextflow run ... + + Some output where something broke + + - type: textarea + id: files + attributes: + label: Relevant files + description: | + Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed. + Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files. + + - type: textarea + id: system + attributes: + label: System information + description: | + * Nextflow version _(eg. 23.04.0)_ + * Hardware _(eg. HPC, Desktop, Cloud)_ + * 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 sanger-tol/longreadmag _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml new file mode 100644 index 0000000..0e9fe29 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -0,0 +1,11 @@ +name: Feature request +description: Suggest an idea for the sanger-tol/longreadmag pipeline +labels: enhancement +body: + - type: textarea + id: description + attributes: + label: Description of feature + description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. + validations: + required: true diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..cb4e2be --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,25 @@ + + +## 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/sanger-tol/longreadmag/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 `). +- [ ] Usage Documentation in `docs/usage.md` is updated. +- [ ] Output Documentation in `docs/output.md` is updated. +- [ ] `CHANGELOG.md` is updated. +- [ ] `README.md` is updated (including new tool citations and authors/contributors). diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml new file mode 100644 index 0000000..56a6c44 --- /dev/null +++ b/.github/workflows/branch.yml @@ -0,0 +1,44 @@ +name: nf-core branch protection +# This workflow is triggered on PRs to master branch on the repository +# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +on: + pull_request_target: + branches: [master] + +jobs: + test: + runs-on: ubuntu-latest + steps: + # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + - name: Check PRs + if: github.repository == 'sanger-tol/longreadmag' + run: | + { [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/longreadmag ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + + # If the above check failed, post a comment on the PR explaining the failure + # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets + - name: Post PR comment + if: failure() + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + with: + message: | + ## This PR is against the `master` branch :x: + + * Do not close this PR + * Click _Edit_ and change the `base` to `dev` + * This CI test will remain failed until you push a new commit + + --- + + Hi @${{ github.event.pull_request.user.login }}, + + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. + The `master` branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + + You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. + Note that even after this, the test will continue to show as failing until you push a new commit. + + Thanks again for your contribution! + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..acb5179 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,85 @@ +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 == 'sanger-tol/longreadmag') }}" + runs-on: ubuntu-latest + strategy: + matrix: + NXF_VER: + - "24.04.2" + - "latest-everything" + profile: + - "conda" + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Set up Nextflow + uses: nf-core/setup-nextflow@v2 + with: + version: "${{ 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 }}" + 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 new file mode 100644 index 0000000..0b6b1f2 --- /dev/null +++ b/.github/workflows/clean-up.yml @@ -0,0 +1,24 @@ +name: "Close user-tagged issues and PRs" +on: + schedule: + - cron: "0 0 * * 0" # Once a week + +jobs: + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 + with: + stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." + stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml new file mode 100644 index 0000000..713dc3e --- /dev/null +++ b/.github/workflows/download_pipeline.yml @@ -0,0 +1,119 @@ +name: Test successful pipeline download with 'nf-core pipelines download' + +# Run the workflow when: +# - dispatched manually +# - when a PR is opened or reopened to master branch +# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. +on: + workflow_dispatch: + inputs: + testbranch: + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." + required: true + default: "dev" + pull_request: + types: + - opened + - edited + - synchronize + branches: + - master + pull_request_target: + branches: + - master + +env: + NXF_ANSI_LOG: false + +jobs: + download: + runs-on: ubuntu-latest + steps: + - name: Install Nextflow + uses: nf-core/setup-nextflow@v2 + + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + with: + python-version: "3.12" + architecture: "x64" + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 + with: + apptainer-version: 1.3.4 + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install git+https://github.com/nf-core/tools.git@dev + + - name: Get the repository name and current branch set as environment variable + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + + - name: Download the pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + run: | + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ + --revision ${{ env.REPO_BRANCH }} \ + --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + --compress "none" \ + --container-system 'singularity' \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ + --container-cache-utilisation 'amend' \ + --download-configuration 'yes' + + - name: Inspect download + run: tree ./${{ env.REPOTITLE_LOWERCASE }} + + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + + - name: Run the downloaded pipeline (stub) + id: stub_run_pipeline + continue-on-error: true + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + - name: Run the downloaded pipeline (stub run not supported) + id: run_pipeline + if: ${{ job.steps.stub_run_pipeline.status == failure() }} + env: + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml new file mode 100644 index 0000000..5cd875c --- /dev/null +++ b/.github/workflows/fix-linting.yml @@ -0,0 +1,89 @@ +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 == 'sanger-tol/longreadmag' + runs-on: ubuntu-latest + steps: + # Use the @nf-core-bot token to check out so we can push later + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # 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@82c7e631bb3cdc910f68e0081d67478d79c6982d # 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/sanger-tol/longreadmag/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml new file mode 100644 index 0000000..a502573 --- /dev/null +++ b/.github/workflows/linting.yml @@ -0,0 +1,83 @@ +name: nf-core linting +# This workflow is triggered on pushes and PRs to the repository. +# 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@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # 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: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Install Nextflow + uses: nf-core/setup-nextflow@v2 + + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + with: + python-version: "3.12" + architecture: "x64" + + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + + - name: Save PR number + if: ${{ always() }} + run: echo ${{ github.event.pull_request.number }} > PR_number.txt + + - name: Upload linting log file artifact + if: ${{ always() }} + uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + with: + name: linting-logs + path: | + lint_log.txt + lint_results.md + PR_number.txt diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml new file mode 100644 index 0000000..42e519b --- /dev/null +++ b/.github/workflows/linting_comment.yml @@ -0,0 +1,28 @@ +name: nf-core linting comment +# This workflow is triggered after the linting action is complete +# It posts an automated comment to the PR, even if the PR is coming from a fork + +on: + workflow_run: + workflows: ["nf-core linting"] + +jobs: + test: + runs-on: ubuntu-latest + steps: + - name: Download lint results + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 + with: + workflow: linting.yml + workflow_conclusion: completed + + - name: Get PR number + id: pr_number + run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT + + - name: Post PR comment + uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 + with: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + number: ${{ steps.pr_number.outputs.pr_number }} + path: linting-logs/lint_results.md diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 0000000..e8aafe4 --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,46 @@ +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@0ad4b8fadaa221de15dcec353f45205ec38ea70b # 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/.nf-core.yml b/.nf-core.yml index 0894f4b..83f0a8a 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,107 +1,105 @@ bump_version: null lint: files_exist: - - .github/ISSUE_TEMPLATE/bug_report.yml - - .github/ISSUE_TEMPLATE/feature_request.yml - - .github/PULL_REQUEST_TEMPLATE.md - - .github/CONTRIBUTING.md - - .github/.dockstore.yml - - conf/igenomes.config - - conf/igenomes_ignored.config - - conf/igenomes.config - - assets/email_template.html - - assets/sendmail_template.txt - - assets/email_template.txt - - .github/ISSUE_TEMPLATE/bug_report.yml - - .github/ISSUE_TEMPLATE/feature_request.yml - - .github/PULL_REQUEST_TEMPLATE.md - - .github/CONTRIBUTING.md - - .github/.dockstore.yml - - conf/igenomes.config - - conf/igenomes_ignored.config - - assets/email_template.html - - assets/sendmail_template.txt - - assets/email_template.txt - - CODE_OF_CONDUCT.md - - assets/nf-core-longreadmag_logo_light.png - - docs/images/nf-core-longreadmag_logo_light.png - - docs/images/nf-core-longreadmag_logo_dark.png - - .github/ISSUE_TEMPLATE/config.yml - - .github/workflows/awstest.yml - - .github/workflows/awsfulltest.yml + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/ISSUE_TEMPLATE/feature_request.yml + - .github/PULL_REQUEST_TEMPLATE.md + - .github/CONTRIBUTING.md + - .github/.dockstore.yml + - conf/igenomes.config + - conf/igenomes_ignored.config + - conf/igenomes.config + - assets/email_template.html + - assets/sendmail_template.txt + - assets/email_template.txt + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/ISSUE_TEMPLATE/feature_request.yml + - .github/PULL_REQUEST_TEMPLATE.md + - .github/CONTRIBUTING.md + - .github/.dockstore.yml + - conf/igenomes.config + - conf/igenomes_ignored.config + - assets/email_template.html + - assets/sendmail_template.txt + - assets/email_template.txt + - CODE_OF_CONDUCT.md + - assets/nf-core-longreadmag_logo_light.png + - docs/images/nf-core-longreadmag_logo_light.png + - docs/images/nf-core-longreadmag_logo_dark.png + - .github/ISSUE_TEMPLATE/config.yml + - .github/workflows/awstest.yml + - .github/workflows/awsfulltest.yml files_unchanged: - - .github/ISSUE_TEMPLATE/bug_report.yml - - .github/ISSUE_TEMPLATE/config.yml - - .github/ISSUE_TEMPLATE/feature_request.yml - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/branch.yml - - .github/workflows/linting_comment.yml - - .github/workflows/linting.yml - - .github/CONTRIBUTING.md - - .github/.dockstore.yml - - .github/CONTRIBUTING.md - - .prettierignore - - .prettierignore - - .prettierignore - - .github/ISSUE_TEMPLATE/bug_report.yml - - .github/ISSUE_TEMPLATE/config.yml - - .github/ISSUE_TEMPLATE/feature_request.yml - - .github/PULL_REQUEST_TEMPLATE.md - - .github/workflows/branch.yml - - .github/workflows/linting_comment.yml - - .github/workflows/linting.yml - - .github/CONTRIBUTING.md - - .github/.dockstore.yml - - .github/CONTRIBUTING.md - - .prettierignore - - .prettierignore - - .prettierignore - - CODE_OF_CONDUCT.md - - assets/nf-core-longreadmag_logo_light.png - - docs/images/nf-core-longreadmag_logo_light.png - - docs/images/nf-core-longreadmag_logo_dark.png - - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/ISSUE_TEMPLATE/config.yml + - .github/ISSUE_TEMPLATE/feature_request.yml + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - .github/CONTRIBUTING.md + - .github/.dockstore.yml + - .github/CONTRIBUTING.md + - .prettierignore + - .prettierignore + - .prettierignore + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/ISSUE_TEMPLATE/config.yml + - .github/ISSUE_TEMPLATE/feature_request.yml + - .github/PULL_REQUEST_TEMPLATE.md + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - .github/CONTRIBUTING.md + - .github/.dockstore.yml + - .github/CONTRIBUTING.md + - .prettierignore + - .prettierignore + - .prettierignore + - CODE_OF_CONDUCT.md + - assets/nf-core-longreadmag_logo_light.png + - docs/images/nf-core-longreadmag_logo_light.png + - docs/images/nf-core-longreadmag_logo_dark.png + - .github/ISSUE_TEMPLATE/bug_report.yml included_configs: false multiqc_config: - - report_comment + - report_comment nextflow_config: - - process.cpus - - process.memory - - process.time - - custom_config - - params.custom_config_version - - params.custom_config_base - - manifest.name - - manifest.homePage - - validation.help.beforeText - - validation.help.afterText - - validation.summary.beforeText - - validation.summary.afterText + - process.cpus + - process.memory + - process.time + - custom_config + - params.custom_config_version + - params.custom_config_base + - manifest.name + - manifest.homePage + - validation.help.beforeText + - validation.help.afterText + - validation.summary.beforeText + - validation.summary.afterText readme: - - nextflow_badge - - nextflow_badge - - nextflow_badge + - nextflow_badge + - nextflow_badge + - nextflow_badge nf_core_version: 3.0.2 org_path: null repository_type: pipeline template: author: Jim Downie, Will Eagles, Noah Gettle description: Construct MAGs from long reads. - force: true + force: false is_nfcore: false name: longreadmag org: sanger-tol outdir: . skip_features: - - github - - igenomes - - github_badges - - nf_core_configs - - codespaces - - fastqc - - email - - adaptivecard - - slackreport - - seqera_platform + - igenomes + - github_badges + - codespaces + - fastqc + - email + - adaptivecard + - slackreport + - seqera_platform version: 1.0.0dev update: null diff --git a/CITATIONS.md b/CITATIONS.md index 701e683..befebe2 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,8 +10,6 @@ ## Pipeline tools - - - [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/README.md b/README.md index 431243c..e33bf0c 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,3 @@ - - # sanger-tol/longreadmag ## Introduction @@ -16,7 +14,6 @@ workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. --> - 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage diff --git a/docs/output.md b/docs/output.md index c40a7cf..5c3936a 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,12 +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: - - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution - - ### MultiQC
diff --git a/docs/usage.md b/docs/usage.md index ea3a6c4..1b8fdeb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -132,6 +132,8 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. ::: +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). + Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. @@ -185,6 +187,16 @@ To use a different container from the default container or conda environment spe A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. + +### nf-core/configs + +In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile. + +See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files. + +If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). + ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/nextflow.config b/nextflow.config index 22b96cb..113aa05 100644 --- a/nextflow.config +++ b/nextflow.config @@ -33,7 +33,14 @@ params { version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - + // Config options + config_profile_name = null + config_profile_description = null + + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_contact = null + config_profile_url = null // Schema validation default options validate_params = true @@ -145,7 +152,12 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" +// Load sanger-tol/longreadmag custom profiles from different institutions. +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/longreadmag.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 diff --git a/nextflow_schema.json b/nextflow_schema.json index e73cc7c..1012526 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -36,6 +36,54 @@ } } }, + "institutional_config_options": { + "title": "Institutional config options", + "type": "object", + "fa_icon": "fas fa-university", + "description": "Parameters used to describe centralised config profiles. These should not be edited.", + "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", + "properties": { + "custom_config_version": { + "type": "string", + "description": "Git commit id for Institutional configs.", + "default": "master", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "custom_config_base": { + "type": "string", + "description": "Base directory for Institutional configs.", + "default": "https://raw.githubusercontent.com/nf-core/configs/master", + "hidden": true, + "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", + "fa_icon": "fas fa-users-cog" + }, + "config_profile_name": { + "type": "string", + "description": "Institutional config name.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_description": { + "type": "string", + "description": "Institutional config description.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_contact": { + "type": "string", + "description": "Institutional config contact information.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, + "config_profile_url": { + "type": "string", + "description": "Institutional config URL link.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + } + } + }, "generic_options": { "title": "Generic options", "type": "object", @@ -111,8 +159,10 @@ { "$ref": "#/$defs/input_output_options" }, - - + + { + "$ref": "#/$defs/institutional_config_options" + }, { "$ref": "#/$defs/generic_options" } From 6aff733264b93e368fa918c70b7e8fefd0ad8cdb Mon Sep 17 00:00:00 2001 From: Jim Downie Date: Wed, 27 Nov 2024 10:47:48 +0000 Subject: [PATCH 3/3] Fix linting --- conf/co2footprint.config | 3 ++- conf/modules.config | 1 - conf/test.config | 1 - main.nf | 1 - nextflow.config | 5 +---- subworkflows/local/utils_nfcore_longreadmag_pipeline/main.nf | 4 +--- 6 files changed, 4 insertions(+), 11 deletions(-) diff --git a/conf/co2footprint.config b/conf/co2footprint.config index 1fc4f45..b93a93c 100644 --- a/conf/co2footprint.config +++ b/conf/co2footprint.config @@ -6,4 +6,5 @@ co2footprint { file = "${params.outdir}/co2footprint.txt" reportFile = "${params.outdir}/co2footprint_report.html" location = "GB" -} \ No newline at end of file +} + diff --git a/conf/modules.config b/conf/modules.config index 255b138..f0b0d55 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,7 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index e1782d0..54b09ae 100644 --- a/conf/test.config +++ b/conf/test.config @@ -27,5 +27,4 @@ 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_test_illumina_amplicon.csv' - } diff --git a/main.nf b/main.nf index 10fc712..52db0e2 100644 --- a/main.nf +++ b/main.nf @@ -74,7 +74,6 @@ workflow { PIPELINE_COMPLETION ( params.outdir, params.monochrome_logs, - SANGERTOL_LONGREADMAG.out.multiqc_report ) } diff --git a/nextflow.config b/nextflow.config index 113aa05..e51a0e3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -13,8 +13,6 @@ params { // Input options input = null - - // MultiQC options multiqc_config = null multiqc_title = null @@ -26,7 +24,7 @@ params { outdir = null publish_dir_mode = 'copy' monochrome_logs = false - + help = false help_full = false show_hidden = false @@ -235,7 +233,6 @@ validation { command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " fullParameter = "help_full" showHiddenParameter = "show_hidden" - } } diff --git a/subworkflows/local/utils_nfcore_longreadmag_pipeline/main.nf b/subworkflows/local/utils_nfcore_longreadmag_pipeline/main.nf index ef98021..8860cf2 100644 --- a/subworkflows/local/utils_nfcore_longreadmag_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_longreadmag_pipeline/main.nf @@ -101,7 +101,7 @@ workflow PIPELINE_COMPLETION { take: outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output - + multiqc_report // string: Path to MultiQC report main: @@ -149,7 +149,6 @@ def toolCitationText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "MultiQC (Ewels et al. 2016)", "." ].join(' ').trim() @@ -162,7 +161,6 @@ def toolBibliographyText() { // 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 = [ - "
  • 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()