diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 88b788b7..6efa85ad 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,23 +1,23 @@ -# nf-core/plantpathsurveil: Contributing Guidelines +# `nf-core/pathogensurveillance`: Contributing Guidelines Hi there! -Many thanks for taking an interest in improving nf-core/plantpathsurveil. +Many thanks for taking an interest in improving nf-core/pathogensurveillance. -We try to manage the required tasks for nf-core/plantpathsurveil using GitHub issues, you probably came to this page when creating one. +We try to manage the required tasks for nf-core/pathogensurveillance 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/plantpathsurveil then the best place to ask is on the nf-core Slack [#plantpathsurveil](https://nfcore.slack.com/channels/plantpathsurveil) channel ([join our Slack here](https://nf-co.re/join/slack)). +> If you need help using or modifying nf-core/pathogensurveillance then the best place to ask is on the nf-core Slack [#pathogensurveillance](https://nfcore.slack.com/channels/pathogensurveillance) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow -If you'd like to write some code for nf-core/plantpathsurveil, the standard workflow is as follows: +If you'd like to write some code for nf-core/pathogensurveillance, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [nf-core/plantpathsurveil issues](https://github.com/nf-core/plantpathsurveil/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/plantpathsurveil repository](https://github.com/nf-core/plantpathsurveil) to your GitHub account +1. Check that there isn't already an issue about your idea in the [nf-core/pathogensurveillance issues](https://github.com/nf-core/pathogensurveillance/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/pathogensurveillance repository](https://github.com/nf-core/pathogensurveillance) 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 @@ -55,23 +55,23 @@ These tests are run both with the latest available version of `Nextflow` and als :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`. +- On your own fork, make a new branch `patch` based on `upstream/main` or `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. +- Open a pull-request from `patch` to `main`/`master` with the changes. ## Getting help -For further information/help, please consult the [nf-core/plantpathsurveil documentation](https://nf-co.re/plantpathsurveil/usage) and don't hesitate to get in touch on the nf-core Slack [#plantpathsurveil](https://nfcore.slack.com/channels/plantpathsurveil) channel ([join our Slack here](https://nf-co.re/join/slack)). +For further information/help, please consult the [nf-core/pathogensurveillance documentation](https://nf-co.re/pathogensurveillance/usage) and don't hesitate to get in touch on the nf-core Slack [#pathogensurveillance](https://nfcore.slack.com/channels/pathogensurveillance) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Pipeline contribution conventions -To make the nf-core/plantpathsurveil 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 `nf-core/pathogensurveillance` 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 +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). @@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards: ### Default values -Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. +Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. @@ -115,7 +115,7 @@ 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/plantpathsurveil/codespaces) +- Open the repo in [Codespaces](https://github.com/nf-core/pathogensurveillance/codespaces) - Tools installed - nf-core - Nextflow diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 852ff617..3b34dd8e 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -8,7 +8,7 @@ body: Before you post this issue, please check the documentation: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - - [nf-core/plantpathsurveil pipeline documentation](https://nf-co.re/plantpathsurveil/usage) + - [nf-core/pathogensurveillance pipeline documentation](https://nf-co.re/pathogensurveillance/usage) - type: textarea id: description @@ -47,4 +47,4 @@ 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/plantpathsurveil _(eg. 1.1, 1.5, 1.8.2)_ + * Version of nf-core/pathogensurveillance _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index daf4fe27..716aa4e1 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -2,6 +2,6 @@ contact_links: - name: Join nf-core url: https://nf-co.re/join about: Please join the nf-core community here - - name: "Slack #plantpathsurveil channel" - url: https://nfcore.slack.com/channels/plantpathsurveil - about: Discussion about the nf-core/plantpathsurveil pipeline + - name: "Slack #pathogensurveillance channel" + url: https://nfcore.slack.com/channels/pathogensurveillance + about: Discussion about the nf-core/pathogensurveillance pipeline diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index d7974666..9a174f21 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/plantpathsurveil pipeline +description: Suggest an idea for the nf-core/pathogensurveillance pipeline labels: enhancement body: - type: textarea diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 068d5667..9682a3bc 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,22 +1,22 @@ ## 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/plantpathsurveil/tree/master/.github/CONTRIBUTING.md) -- [ ] If necessary, also make a PR on the nf-core/plantpathsurveil _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/nf-core/pathogensurveillance/tree/master/.github/CONTRIBUTING.md) +- [ ] If necessary, also make a PR on the nf-core/pathogensurveillance _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] 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 index 0003d256..2c4e1555 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,11 +1,12 @@ name: nf-core AWS full size tests -# This workflow is triggered on PRs opened against the master branch. +# 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: pull_request: branches: + - main - master workflow_dispatch: pull_request_review: @@ -15,21 +16,33 @@ jobs: run-platform: name: Run AWS full tests # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered - if: github.repository == 'nf-core/plantpathsurveil' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' + if: github.repository == 'nf-core/pathogensurveillance' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - - uses: octokit/request-action@v2.x + - name: Get PR reviews + uses: octokit/request-action@v2.x + if: github.event_name != 'workflow_dispatch' id: check_approvals + continue-on-error: true with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - id: test_variables + + - name: Check for approvals + if: ${{ failure() && github.event_name != 'workflow_dispatch' }} + run: | + echo "No review approvals found. At least 2 approvals are required to run this action automatically." + exit 1 + + - name: Check for enough approvals (>=2) + id: test_variables if: github.event_name != 'workflow_dispatch' run: | JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required @@ -40,11 +53,11 @@ jobs: access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/plantpathsurveil/work-${{ github.sha }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pathogensurveillance/work-${{ github.sha }} parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/plantpathsurveil/results-${{ github.sha }}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pathogensurveillance/results-${{ github.sha }}" } profiles: test_full diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 54128572..b8de0b50 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -7,7 +7,7 @@ on: jobs: run-platform: name: Run AWS tests - if: github.repository == 'nf-core/plantpathsurveil' + if: github.repository == 'nf-core/pathogensurveillance' runs-on: ubuntu-latest steps: # Launch workflow using Seqera Platform CLI tool action @@ -18,10 +18,10 @@ jobs: access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} revision: ${{ github.sha }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/plantpathsurveil/work-${{ github.sha }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pathogensurveillance/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/plantpathsurveil/results-test-${{ github.sha }}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pathogensurveillance/results-test-${{ github.sha }}" } profiles: test diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index b7bc4174..2dd61431 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,19 +1,21 @@ 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` +# This workflow is triggered on PRs to `main`/`master` branch on the repository +# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev` on: pull_request_target: - branches: [master] + branches: + - main + - 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 + # 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/plantpathsurveil' + if: github.repository == 'nf-core/pathogensurveillance' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/plantpathsurveil ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/pathogensurveillance ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets @@ -22,7 +24,7 @@ jobs: uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | - ## This PR is against the `master` branch :x: + ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: * Do not close this PR * Click _Edit_ and change the `base` to `dev` @@ -32,9 +34,9 @@ jobs: 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/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch. + The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bbcd3997..df31904a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,7 +22,7 @@ jobs: test: name: "Run pipeline with test data (${{ 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/plantpathsurveil') }}" + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pathogensurveillance') }}" runs-on: ubuntu-latest strategy: matrix: @@ -45,7 +45,7 @@ jobs: profile: "singularity" steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 713dc3e7..2576cc0c 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to master branch +# - when a PR is opened or reopened to main/master branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: @@ -17,9 +17,11 @@ on: - edited - synchronize branches: + - main - master pull_request_target: branches: + - main - master env: @@ -35,7 +37,7 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" @@ -69,7 +71,7 @@ jobs: --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ --container-cache-utilisation 'amend' \ --download-configuration 'yes' diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 30b09cb3..8b451303 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -9,11 +9,11 @@ jobs: if: > contains(github.event.comment.html_url, '/pull/') && contains(github.event.comment.body, '@nf-core-bot fix linting') && - github.repository == 'nf-core/plantpathsurveil' + github.repository == 'nf-core/pathogensurveillance' runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,7 +32,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" @@ -86,4 +86,4 @@ jobs: 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/plantpathsurveil/actions/runs/${{ github.run_id }}) for more details. + See [CI log](https://github.com/nf-core/pathogensurveillance/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a502573c..dbd52d5a 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" @@ -31,12 +31,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" @@ -74,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 42e519bf..0bed96d3 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@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 + uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c6ba35df..450b1d5e 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -31,7 +31,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.10" - name: Install dependencies diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml index e8aafe44..537529bc 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template_version_comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.gitpod.yml b/.gitpod.yml index 46118637..83599f63 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -6,12 +6,5 @@ tasks: nextflow self-update vscode: - extensions: # based on nf-core.nf-core-extensionpack - #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code - - charliermarsh.ruff # Code linter Ruff + extensions: + - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index e1f3d235..3efc22ad 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,7 +1,4 @@ -bump_version: null -lint: null -nf_core_version: 3.0.2 -org_path: null +nf_core_version: 3.1.0 repository_type: pipeline template: author: "Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I.\ @@ -12,6 +9,4 @@ template: name: pathogensurveillance org: nf-core outdir: . - skip_features: null version: 1.0dev -update: null diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..a33b527c --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "markdown.styles": ["public/vscode_markdown.css"] +} diff --git a/README.md b/README.md index 62a6cfd3..3bd6a6c0 100644 --- a/README.md +++ b/README.md @@ -65,10 +65,18 @@ Now, you can run the pipeline using: nextflow run nf-core/pathogensurveillance -r dev -profile RUN_TOOL -resume --sample_data --out_dir --download_bakta_db ``` +```bash +nextflow run nf-core/pathogensurveillance \ + -profile \ + --input samplesheet.csv \ + --outdir +``` ## Documentation +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/pathogensurveillance/usage) and the [parameter documentation](https://nf-co.re/pathogensurveillance/parameters). + Documentation is currently under development, but can be found here: https://grunwaldlab.github.io/pathogensurveillance_documentation @@ -121,6 +129,14 @@ The reference metadata CSV or the sample metadata CSV can have the following col nf-core/pathogensurveillance was originally written by Zachary S.L. Foster, Camilo Parada-Rojas, Logan Blair, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Ricardo Alcalá-Briseño, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/pathogensurveillance/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/pathogensurveillance/output). + +## Credits + +nf-core/pathogensurveillance was originally written by Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald. + ## Contributions and Support diff --git a/assets/schema_input.json b/assets/schema_input.json index 7712d7b0..94fc658f 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,8 +1,8 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/pathogensurveillance/master/assets/schema_input.json", - "title": "nf-core/pathogensurveillance pipeline - params.sample_data schema", - "description": "Schema for the file provided with params.sample_data", + "title": "nf-core/pathogensurveillance pipeline - params.input schema", + "description": "Schema for the file provided with params.input", "type": "array", "items": { "type": "object", diff --git a/conf/base.config b/conf/base.config index 4a56aef0..7c3c2a99 100644 --- a/conf/base.config +++ b/conf/base.config @@ -19,7 +19,7 @@ process { maxErrors = '-1' // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. + // NOTE - Please try and reuse the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. diff --git a/conf/modules.config b/conf/modules.config index 429fd7bd..c1548503 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -33,8 +33,8 @@ process { } } maxRetries = 1 - - // Only use swap for singularity + + // Only use swap for singularity containerOptions = { workflow.containerEngine == 'singularity' ? '': "--memory-swap ${task.memory.mega.intValue()}m" } diff --git a/docs/usage.md b/docs/usage.md index c5217c08..746092b2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -75,9 +75,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> [!WARNING] +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -106,23 +105,21 @@ nextflow pull nf-core/pathogensurveillance ### Reproducibility -It is a good idea to specify a 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. +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/pathogensurveillance releases page](https://github.com/nf-core/pathogensurveillance/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. -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: +> [!TIP] +> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. ## Core Nextflow arguments -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: +> [!NOTE] +> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen) ### `-profile` @@ -130,16 +127,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: +> [!IMPORTANT] +> 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). +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 check if your system is suported, 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. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment. - `test` - A profile with a complete configuration for automated testing @@ -175,13 +171,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se ### Resource requests -Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. +Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. ### Custom Containers -In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. +In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. diff --git a/main.nf b/main.nf index 1bc97c9f..8fee7a62 100644 --- a/main.nf +++ b/main.nf @@ -1,7 +1,11 @@ #!/usr/bin/env nextflow /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +<<<<<<< HEAD nf-core/PATHOGENSURVEILLANCE +======= + nf-core/pathogensurveillance +>>>>>>> 903bebec0530d13e13bd909528fc81d1cfb62b67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/pathogensurveillance Website: https://nf-co.re/pathogensurveillance @@ -15,9 +19,10 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { PATHOGENSURVEILLANCE } from './workflows/pathogensurveillance' +include { PATHOGENSURVEILLANCE } from './workflows/pathogensurveillance' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_pathogensurveillance_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_pathogensurveillance_pipeline' +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_pathogensurveillance_pipeline' /* diff --git a/modules.json b/modules.json index 00067a86..08711d4c 100644 --- a/modules.json +++ b/modules.json @@ -171,17 +171,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", + "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d8989f48..752c3a10 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -24,7 +24,7 @@ process FASTQC { // 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(' ') + 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 diff --git a/nextflow.config b/nextflow.config index cbd092b0..a59ff6fb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -60,8 +60,7 @@ params { show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - - // 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 @@ -190,6 +189,13 @@ profiles { executor.name = 'local' executor.cpus = 4 executor.memory = 8.GB + process { + resourceLimits = [ + memory: 8.GB, + cpus : 4, + time : 1.h + ] + } } slurm { executor.name = 'slurm' // Use SLURM for job scheduling @@ -267,27 +273,87 @@ if (! params.trace_dir) { } timeline { enabled = true - file = "${params.trace_dir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html" } report { enabled = true - file = "${params.trace_dir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html" } trace { enabled = true - file = "${params.trace_dir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt" } dag { enabled = true - file = "${params.trace_dir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html" } manifest { name = 'nf-core/pathogensurveillance' author = """Zachary S.L. Foster, Camilo Parada-Rojas, Logan Blair, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Ricardo Alcalá-Briseño, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald""" + contributors = [ + // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 + [ + name: 'Zachary S.L. Foster', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: ' Martha Sudermann', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: ' Nicholas C. Cauldron', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: ' Fernanda I. Bocardo', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: ' Hung Phan', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: ' Jeff H. Chang', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: ' Niklaus J. Grünwald', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + ] homePage = 'https://github.com/nf-core/pathogensurveillance' description = """Surveillance of plant pathogens using high-throughput sequencing""" mainScript = 'main.nf' + defaultBranch = 'master' nextflowVersion = '!>=24.04.2' version = '1.0dev' doi = '' @@ -300,9 +366,10 @@ plugins { validation { defaultIgnoreParams = ["genomes"] + monochromeLogs = params.monochrome_logs help { enabled = true - command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + command = "nextflow run nf-core/pathogensurveillance -profile --input samplesheet.csv --outdir " fullParameter = "help_full" showHiddenParameter = "show_hidden" beforeText = """ @@ -312,15 +379,15 @@ validation { \033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m \033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m \033[0;32m`._,._,\'\033[0m -\033[0;35m ${manifest.name} ${manifest.version}\033[0m +\033[0;35m nf-core/pathogensurveillance ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} + afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/nf-core/pathogensurveillance/blob/master/CITATIONS.md """ } summary { diff --git a/nextflow_schema.json b/nextflow_schema.json index 06bed197..e69f6050 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -410,6 +410,12 @@ "description": "Base URL or local path to location of pipeline test dataset files", "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", "hidden": true + }, + "trace_report_suffix": { + "type": "string", + "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 } } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json new file mode 100644 index 00000000..0db2f9a4 --- /dev/null +++ b/ro-crate-metadata.json @@ -0,0 +1,311 @@ +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + { + "GithubService": "https://w3id.org/ro/terms/test#GithubService", + "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", + "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", + "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", + "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", + "TestService": "https://w3id.org/ro/terms/test#TestService", + "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", + "TravisService": "https://w3id.org/ro/terms/test#TravisService", + "definition": "https://w3id.org/ro/terms/test#definition", + "engineVersion": "https://w3id.org/ro/terms/test#engineVersion", + "instance": "https://w3id.org/ro/terms/test#instance", + "resource": "https://w3id.org/ro/terms/test#resource", + "runsOn": "https://w3id.org/ro/terms/test#runsOn" + } + ], + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "creativeWorkStatus": "InProgress", + "datePublished": "2024-12-12T11:24:09+00:00", + "description": "

\n \n \n \"nf-core/pathogensurveillance\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/pathogensurveillance/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pathogensurveillance/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/pathogensurveillance/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pathogensurveillance/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/pathogensurveillance/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/pathogensurveillance)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pathogensurveillance-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pathogensurveillance)[![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/pathogensurveillance** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\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 nf-core/pathogensurveillance \\\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/pathogensurveillance/usage) and the [parameter documentation](https://nf-co.re/pathogensurveillance/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/pathogensurveillance/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/pathogensurveillance/output).\n\n## Credits\n\nnf-core/pathogensurveillance was originally written by Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Hung Phan, Je\ufb00 H. Chang, Niklaus J. Gr\u00fcnwald.\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 `#pathogensurveillance` channel](https://nfcore.slack.com/channels/pathogensurveillance) (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", + "hasPart": [ + { + "@id": "main.nf" + }, + { + "@id": "assets/" + }, + { + "@id": "conf/" + }, + { + "@id": "docs/" + }, + { + "@id": "docs/images/" + }, + { + "@id": "modules/" + }, + { + "@id": "modules/nf-core/" + }, + { + "@id": "workflows/" + }, + { + "@id": "subworkflows/" + }, + { + "@id": "nextflow.config" + }, + { + "@id": "README.md" + }, + { + "@id": "nextflow_schema.json" + }, + { + "@id": "CHANGELOG.md" + }, + { + "@id": "LICENSE" + }, + { + "@id": "CODE_OF_CONDUCT.md" + }, + { + "@id": "CITATIONS.md" + }, + { + "@id": "modules.json" + }, + { + "@id": "docs/usage.md" + }, + { + "@id": "docs/output.md" + }, + { + "@id": ".nf-core.yml" + }, + { + "@id": ".pre-commit-config.yaml" + }, + { + "@id": ".prettierignore" + } + ], + "isBasedOn": "https://github.com/nf-core/pathogensurveillance", + "license": "MIT", + "mainEntity": { + "@id": "main.nf" + }, + "mentions": [ + { + "@id": "#598ddf3a-acab-4cd9-8387-3326bcf18888" + } + ], + "name": "nf-core/pathogensurveillance" + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "main.nf", + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "creator": [ + { + "@id": "#zacharyfoster1989@gmail.com" + } + ], + "dateCreated": "", + "dateModified": "2024-12-12T11:24:09Z", + "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", + "keywords": ["nf-core", "nextflow"], + "license": ["MIT"], + "maintainer": [ + { + "@id": "#zacharyfoster1989@gmail.com" + } + ], + "name": ["nf-core/pathogensurveillance"], + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" + }, + "sdPublisher": { + "@id": "https://nf-co.re/" + }, + "url": ["https://github.com/nf-core/pathogensurveillance", "https://nf-co.re/pathogensurveillance/dev/"], + "version": ["1.0dev"] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", + "@type": "ComputerLanguage", + "identifier": { + "@id": "https://www.nextflow.io/" + }, + "name": "Nextflow", + "url": { + "@id": "https://www.nextflow.io/" + }, + "version": "!>=24.04.2" + }, + { + "@id": "#598ddf3a-acab-4cd9-8387-3326bcf18888", + "@type": "TestSuite", + "instance": [ + { + "@id": "#f7231363-0b1e-473e-9b23-6a0c6398dc8e" + } + ], + "mainEntity": { + "@id": "main.nf" + }, + "name": "Test suite for nf-core/pathogensurveillance" + }, + { + "@id": "#f7231363-0b1e-473e-9b23-6a0c6398dc8e", + "@type": "TestInstance", + "name": "GitHub Actions workflow for testing nf-core/pathogensurveillance", + "resource": "repos/nf-core/pathogensurveillance/actions/workflows/ci.yml", + "runsOn": { + "@id": "https://w3id.org/ro/terms/test#GithubService" + }, + "url": "https://api.github.com" + }, + { + "@id": "https://w3id.org/ro/terms/test#GithubService", + "@type": "TestService", + "name": "Github Actions", + "url": { + "@id": "https://github.com" + } + }, + { + "@id": "assets/", + "@type": "Dataset", + "description": "Additional files" + }, + { + "@id": "conf/", + "@type": "Dataset", + "description": "Configuration files" + }, + { + "@id": "docs/", + "@type": "Dataset", + "description": "Markdown files for documenting the pipeline" + }, + { + "@id": "docs/images/", + "@type": "Dataset", + "description": "Images for the documentation files" + }, + { + "@id": "modules/", + "@type": "Dataset", + "description": "Modules used by the pipeline" + }, + { + "@id": "modules/nf-core/", + "@type": "Dataset", + "description": "nf-core modules" + }, + { + "@id": "workflows/", + "@type": "Dataset", + "description": "Main pipeline workflows to be executed in main.nf" + }, + { + "@id": "subworkflows/", + "@type": "Dataset", + "description": "Smaller subworkflows" + }, + { + "@id": "nextflow.config", + "@type": "File", + "description": "Main Nextflow configuration file" + }, + { + "@id": "README.md", + "@type": "File", + "description": "Basic pipeline usage information" + }, + { + "@id": "nextflow_schema.json", + "@type": "File", + "description": "JSON schema for pipeline parameter specification" + }, + { + "@id": "CHANGELOG.md", + "@type": "File", + "description": "Information on changes made to the pipeline" + }, + { + "@id": "LICENSE", + "@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", + "description": "Citations needed when using the pipeline" + }, + { + "@id": "modules.json", + "@type": "File", + "description": "Version information for modules from nf-core/modules" + }, + { + "@id": "docs/usage.md", + "@type": "File", + "description": "Usage documentation" + }, + { + "@id": "docs/output.md", + "@type": "File", + "description": "Output documentation" + }, + { + "@id": ".nf-core.yml", + "@type": "File", + "description": "nf-core configuration file, configuring template features and linting rules" + }, + { + "@id": ".pre-commit-config.yaml", + "@type": "File", + "description": "Configuration file for pre-commit hooks" + }, + { + "@id": ".prettierignore", + "@type": "File", + "description": "Ignore file for prettier" + }, + { + "@id": "https://nf-co.re/", + "@type": "Organization", + "name": "nf-core", + "url": "https://nf-co.re/" + }, + { + "@id": "#zacharyfoster1989@gmail.com", + "@type": "Person", + "email": "zacharyfoster1989@gmail.com", + "name": "Zachary S.L. Foster" + } + ] +} diff --git a/subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf b/subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf index 635badb6..b5620a53 100644 --- a/subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pathogensurveillance_pipeline/main.nf @@ -116,7 +116,8 @@ workflow PIPELINE_COMPLETION { main: summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - + def multiqc_reports = multiqc_report.toList() + // // Completion email and summary // @@ -129,7 +130,7 @@ workflow PIPELINE_COMPLETION { plaintext_email, outdir, monochrome_logs, - multiqc_report.toList() + multiqc_reports.getVal(), ) } @@ -225,7 +226,7 @@ def toolBibliographyText() { } def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + // 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() diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 0fcbf7b3..d6e593e8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -92,10 +92,12 @@ def checkCondaChannels() { channels = config.channels } catch (NullPointerException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } catch (IOException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce8..02dbf094 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 5cb7bafe..bfd25876 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) { } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - def manifest_doi = workflow.manifest.doi.tokenize(",") - // Handling 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 - manifest_doi.each { doi_ref -> - temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // @@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) { return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // @@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) { return colorcodes } -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") - } - mqc_report = mqc_report[0] - } +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - catch (Exception all) { - if (multiqc_report) { - log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") - } - } - return mqc_report } // @@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) @@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi if (email_address) { try { if (plaintext_email) { -new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } ['sendmail', '-t'].execute() << sendmail_html log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") } - catch (Exception all) { + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f8..f117040c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,26 +41,14 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { + test("Test Function without logColours") { - function "nfCoreLogo" + function "logColours" when { function { """ - input[0] = false + input[0] = true """ } } @@ -73,9 +61,8 @@ nextflow_function { } } - test("Test Function dashedLine") { - - function "dashedLine" + test("Test Function with logColours") { + function "logColours" when { function { @@ -93,14 +80,13 @@ nextflow_function { } } - test("Test Function without logColours") { - - function "logColours" + test("Test Function getSingleReport with a single file") { + function "getSingleReport" when { function { """ - input[0] = true + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) """ } } @@ -108,18 +94,22 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") } ) } } - test("Test Function with logColours") { - function "logColours" + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" when { function { """ - input[0] = false + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] """ } } @@ -127,7 +117,9 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 1037232c..02c67014 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -17,26 +17,6 @@ }, "timestamp": "2024-02-28T12:02:59.729647" }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, "Test Function without logColours": { "content": [ { @@ -95,16 +75,6 @@ }, "timestamp": "2024-02-28T12:03:17.969323" }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, "Test Function with logColours": { "content": [ { 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 842dc432..8fb30164 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { diff --git a/workflows/pathogensurveillance.nf b/workflows/pathogensurveillance.nf index 692c9e0c..8337aa4f 100644 --- a/workflows/pathogensurveillance.nf +++ b/workflows/pathogensurveillance.nf @@ -17,6 +17,9 @@ include { RECORD_MESSAGES } from '../modules/local/record_messages' include { DOWNLOAD_ASSEMBLIES } from '../modules/local/download_assemblies' include { PREPARE_REPORT_INPUT } from '../modules/local/prepare_report_input' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_pathogensurveillance_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~