Merge pull request #11 from phac-nml/dev

Release 0.2.0

.devcontainer/devcontainer.json

@@ -0,0 +1,20 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}

.editorconfig

@@ -0,0 +1,38 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js}]
+indent_size = 2
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
+[/assets/email*]
+indent_size = unset
+
+# ignore python and markdown
+[*.{py,md}]
+indent_style = unset
+
+# ignore tests
+[*.test]
+indent_style = unset
+end_of_line = unset

.gitattributes

@@ -0,0 +1,4 @@
+*.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,22 @@
+<!--
+# phac-nml/legiovue pull request
+
+Many thanks for contributing to phac-nml/legiovue!
+
+Please fill in the appropriate checklist below (delete whatever is not relevant).
+These are the most common things requested on pull requests (PRs).
+
+Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
+-->
+
+## 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!
+- [ ] Make sure your code lints (`nf-core pipelines lint`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <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).

.github/workflows/branch.yml

@@ -0,0 +1,44 @@
+name: nf-core branch protection
+# This workflow is triggered on PRs to main branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
+on:
+  pull_request_target:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      - name: Check PRs
+        if: github.repository == 'phac-nml/legiovue'
+        run: |
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/legiovue ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+      # If the above check failed, post a comment on the PR explaining the failure
+      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+      - name: Post PR comment
+        if: failure()
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        with:
+          message: |
+            ## This PR is against the `main` branch :x:
+
+            * Do not close this PR
+            * Click _Edit_ and change the `base` to `dev`
+            * This CI test will remain failed until you push a new commit
+
+            ---
+
+            Hi @${{ 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 }}) `main` branch.
+            The `main` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `main` 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

.github/workflows/ci.yml

@@ -0,0 +1,58 @@
+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 }} | ${{ matrix.test_name }} | docker)"
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'phac-nml/legiovue') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.10.1"
+          - "latest-everything"
+        test_name:
+          - "test_full"
+          - "test"
+    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: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://get.nf-test.com | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
+        run: |
+          nf-test test --verbose
+
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | docker"
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},docker --outdir ./results

.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 != 'main' }}
+        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 == 'main' }}
+        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

.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

.gitignore

@@ -5,3 +5,7 @@ results/
 testing/
 testing*
 *.pyc
+null/
+slurm*
+.nf-test.log
+.nf-test/

.nf-core.yml

@@ -1 +1,38 @@
 repository_type: pipeline
+nf_core_version: "3.0.2"
+bump_version: null
+lint:
+  files_exist:
+    - CODE_OF_CONDUCT.md
+    - .github/.dockstore.yml
+    - .github/CONTRIBUTING.md
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/ISSUE_TEMPLATE/feature_request.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - assets/email_template.html
+    - assets/email_template.txt
+    - assets/multiqc_config.yml
+    - assets/sendmail_template.txt
+    - assets/nf-core-LegioVue_logo_light.png
+    - conf/igenomes.config
+    - conf/igenomes_ignored.config
+    - docs/images/nf-core-LegioVue_logo_light.png
+    - docs/images/nf-core-LegioVue_logo_dark.png
+  files_unchanged:
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting.yml
+    - docs/README.md
+    - LICENSE
+    - .gitignore
+  multiqc_config: False
+  pipeline_name_conventions: False
+  actions_awsfulltest: False
+  actions_awstest: False
+  readme: False
+  nextflow_config: False
+
+template:
+  prefix: phac-nml

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "3.0.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec

.prettierignore

@@ -0,0 +1,12 @@
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
+bin/
+adaptivecard.json
+slackreport.json
+tests/

.prettierrc.yml

@@ -0,0 +1 @@
+printWidth: 120