fixed prettier errors

nf-core · Nov 7, 2024 · 5c65c21 · 5c65c21
2 parents 31a28e7 + c7cc952
commit 5c65c21
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/mcmicro, the standard workflow is a
 1. Check that there isn't already an issue about your idea in the [nf-core/mcmicro issues](https://github.com/nf-core/mcmicro/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/mcmicro repository](https://github.com/nf-core/mcmicro) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
-4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
+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/).
@@ -40,7 +40,7 @@ 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 lint <pipeline-directory>` command.
+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 <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
 
@@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards:
 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 schema build` tool).
+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`.
@@ -86,11 +86,11 @@ If you wish to contribute a new step, please use the following coding standards:
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
 
-Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
+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/master/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.
+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.
 
@@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 ### 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 bump-version --nextflow . [min-nf-version]`
+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
 

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mcmi
 - [ ] 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/mcmicro/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/mcmicro _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
-- [ ] Make sure your code lints (`nf-core lint`).
+- [ ] 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.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -1,18 +1,35 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  pull_request:
+    branches:
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
   run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/mcmicro'
+    # 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/mcmicro' && 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
+        id: check_approvals
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
+        run: |
+          JSON_RESPONSE='${{ 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

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -23,7 +23,6 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-
   nf-test-changes:
     name: Check for changes
     runs-on: ubuntu-latest
@@ -51,7 +50,8 @@ jobs:
   test:
     name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})"
     needs: [nf-test-changes]
-    if: needs.nf-test-changes.outputs.nf_test_files != '[]'
+    # 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/mcmicro')) && needs.nf-test-changes.outputs.nf_test_files != '[]' }}"
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -63,9 +63,18 @@ jobs:
         profile:
           # - "conda"
           - "docker"
-          # - "singularity"
+          - "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: install curl
         run: sudo apt update && sudo apt install -y curl wget
 
@@ -77,123 +86,123 @@ jobs:
         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: Install nf-test
-        uses: nf-core/setup-nf-test@v1
-        with:
-          version: ${{ env.NFT_VER }}
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
 
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          architecture: "x64"
-
-      - name: Install pdiff to see diff between nf-test snapshots
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
         run: |
-          python -m pip install --upgrade pip
-          pip install pdiff
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: Run nf-test
-        run: |
-          nf-test test \
-            --verbose ${{ matrix.nf_test_files }} \
-            --profile "+${{ matrix.profile }},ci" \
-            --junitxml=test.xml \
-            --tap=test.tap
-
-      - uses: pcolby/tap-summary@v1
+          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: Install nf-test
+  #        uses: nf-core/setup-nf-test@v1
+  #        with:
+  #          version: ${{ env.NFT_VER }}
+  #
+  #      - uses: actions/setup-python@v4
+  #        with:
+  #          python-version: "3.11"
+  #          architecture: "x64"
+  #
+  #      - name: Install pdiff to see diff between nf-test snapshots
+  #        run: |
+  #          python -m pip install --upgrade pip
+  #          pip install pdiff
+  #
+  #      - name: Clean up Disk space
+  #        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+  #
+  #      - name: Run nf-test
+  #        run: |
+  #          nf-test test \
+  #            --verbose ${{ matrix.nf_test_files }} \
+  #            --profile "+${{ matrix.profile }},ci" \
+  #            --junitxml=test.xml \
+  #            --tap=test.tap
+  #
+  #      - uses: pcolby/tap-summary@v1
+  #        with:
+  #          path: >-
+  #            test.tap
+  #
+  #      - name: Output log on failure
+  #        if: failure()
+  #        run: |
+  #          sudo apt install bat > /dev/null
+  #          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+  #
+  #      - name: Publish Test Report
+  #        uses: mikepenz/action-junit-report@v3
+  #        if: always() # always run even if the previous step fails
+  #        with:
+  #          report_paths: test.xml
+
+  #  confirm-pass:
+  #    runs-on: ubuntu-latest
+  #    needs: [test]
+  #    if: always()
+  #    steps:
+  #      - name: All tests ok
+  #        if: ${{ !contains(needs.*.result, 'failure') }}
+  #        run: exit 0
+  #      - name: One or more tests failed
+  #        if: ${{ contains(needs.*.result, 'failure') }}
+  #        run: exit 1
+  #
+  #      - name: debug-print
+  #        if: always()
+  #        run: |
+  #          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+  #          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+
+  test_orig:
+    name: Run pipeline with test data
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mcmicro') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-java@v4
         with:
-          path: >-
-            test.tap
+          distribution: "zulu" # See 'Supported distributions' for available options
+          java-version: "21"
 
-      - name: Output log on failure
-        if: failure()
-        run: |
-          sudo apt install bat > /dev/null
-          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+      - name: Check out pipeline code
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
-        if: always() # always run even if the previous step fails
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
         with:
-          report_paths: test.xml
+          version: "${{ matrix.NXF_VER }}"
 
-  confirm-pass:
-    runs-on: ubuntu-latest
-    needs: [test]
-    if: always()
-    steps:
-      - name: All tests ok
-        if: ${{ !contains(needs.*.result, 'failure') }}
-        run: exit 0
-      - name: One or more tests failed
-        if: ${{ contains(needs.*.result, 'failure') }}
-        run: exit 1
-
-      - name: debug-print
-        if: always()
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Run pipeline with test data
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        # For example: adding multiple test runs with different parameters
+        # Remember that you can parallelise this by using strategy.matrix
         run: |
-          echo "toJSON(needs) = ${{ toJSON(needs) }}"
-          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
-
-#  test_orig:
-#    name: Run pipeline with test data
-#    # Only run on push if this is the nf-core dev branch (merged PRs)
-#    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mcmicro') }}"
-#    runs-on: ubuntu-latest
-#    strategy:
-#      matrix:
-#        NXF_VER:
-#          - "23.04.0"
-#          - "latest-everything"
-#    steps:
-#      - uses: actions/checkout@v4
-#      - uses: actions/setup-java@v4
-#        with:
-#          distribution: 'zulu' # See 'Supported distributions' for available options
-#          java-version: '21'
-#
-#      - name: Check out pipeline code
-#        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-#
-#      - name: Install Nextflow
-#        uses: nf-core/setup-nextflow@v2
-#        with:
-#          version: "${{ matrix.NXF_VER }}"
-#
-#      - name: Disk space cleanup
-#        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-#
-#      - name: Run pipeline with test data
-#        # TODO nf-core: You can customise CI pipeline run tests as required
-#        # For example: adding multiple test runs with different parameters
-#        # Remember that you can parallelise this by using strategy.matrix
-#        run: |
-#          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results