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Merge pull request #601 from nf-core/dev
Release 2.6.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,5 @@ | ||
| *.config linguist-language=nextflow | ||
| *.nf.test linguist-language=nextflow | ||
| tests/**/*nf.test.snap linguist-generated | ||
| modules/nf-core/** linguist-generated | ||
| subworkflows/nf-core/** linguist-generated |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,74 +1,106 @@ | ||
| name: nf-core CI | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| name: nf-core CI | ||
| on: | ||
| push: | ||
| branches: | ||
| - dev | ||
| - "dev" | ||
| pull_request: | ||
| branches: | ||
| - "dev" | ||
| - "master" | ||
| release: | ||
| types: [published] | ||
| types: | ||
| - "published" | ||
|
|
||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.7.3" | ||
|
|
||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| define_nxf_versions: | ||
| name: Choose nextflow versions to test against depending on target branch | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| matrix: ${{ steps.nxf_versions.outputs.matrix }} | ||
| steps: | ||
| - id: nxf_versions | ||
| run: | | ||
| if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then | ||
| echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT | ||
| else | ||
| echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT | ||
| fi | ||
| test: | ||
| name: Run pipeline with test data | ||
| # Only run on push if this is the nf-core dev branch (merged PRs) | ||
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/ampliseq') }}" | ||
| name: nf-test | ||
| needs: define_nxf_versions | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "22.10.1" | ||
| - "latest-everything" | ||
| NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} | ||
| tags: | ||
| - "test" | ||
| - "test_single" | ||
| - "test_fasta" | ||
| - "test_multi" | ||
| - "test_reftaxcustom" | ||
| - "test_doubleprimers" | ||
| - "test_iontorrent" | ||
| - "test_novaseq" | ||
| - "test_pacbio_its" | ||
| - "test_sintax" | ||
| - "test_pplace" | ||
| profile: | ||
| - "docker" | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Check out test data | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| repository: nf-core/test-datasets | ||
| ref: ampliseq | ||
| path: test-datasets/ | ||
| fetch-depth: 1 | ||
|
|
||
| - name: Replace remote paths in samplesheets | ||
| run: | | ||
| for f in ${{ github.workspace }}/test-datasets/samplesheets/*.tsv; do | ||
| sed -i "s=https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/=${{ github.workspace }}/test-datasets/=g" $f | ||
| echo "========== $f ============" | ||
| cat $f | ||
| echo "========================================" | ||
| done; | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Run pipeline with test data | ||
| - name: Install nf-test | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | ||
| wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER | ||
| sudo mv nf-test /usr/local/bin/ | ||
| profiles: | ||
| name: Run workflow 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/ampliseq') }} | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| # Run remaining test profiles with minimum nextflow version | ||
| profile: | ||
| [ | ||
| test_multi, | ||
| test_pacbio_its, | ||
| test_doubleprimers, | ||
| test_iontorrent, | ||
| test_single, | ||
| test_fasta, | ||
| test_reftaxcustom, | ||
| test_novaseq, | ||
| ] | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Install Nextflow | ||
| - name: Run nf-test | ||
| run: | | ||
| wget -qO- get.nextflow.io | bash | ||
| sudo mv nextflow /usr/local/bin/ | ||
| nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml | ||
| - name: Run pipeline with ${{ matrix.profile }} test profile | ||
| - name: Output log on failure | ||
| if: failure() | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results | ||
| sudo apt install bat > /dev/null | ||
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml | ||
| # | ||
| - name: Publish Test Report | ||
| uses: mikepenz/action-junit-report@v3 | ||
| if: always() # always run even if the previous step fails | ||
| with: | ||
| report_paths: "*.xml" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| name: "Close user-tagged issues and PRs" | ||
| on: | ||
| schedule: | ||
| - cron: "0 0 * * 0" # Once a week | ||
|
|
||
| jobs: | ||
| clean-up: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| issues: write | ||
| pull-requests: write | ||
| steps: | ||
| - uses: actions/stale@v7 | ||
| with: | ||
| stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." | ||
| stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." | ||
| close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." | ||
| days-before-stale: 30 | ||
| days-before-close: 20 | ||
| days-before-pr-close: -1 | ||
| any-of-labels: "awaiting-changes,awaiting-feedback" | ||
| exempt-issue-labels: "WIP" | ||
| exempt-pr-labels: "WIP" | ||
| repo-token: "${{ secrets.GITHUB_TOKEN }}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -12,3 +12,5 @@ testing* | |
| .screenrc | ||
| ampliseq.Rproj | ||
| results_test/* | ||
| .nf-test/ | ||
| nf-test | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,7 @@ | ||
| repository_type: pipeline | ||
|
|
||
| lint: | ||
| files_unchanged: | ||
| - .gitattributes | ||
| files_exist: | ||
| - conf/igenomes.config | ||
| actions_ci: False |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/mirrors-prettier | ||
| rev: "v2.7.1" | ||
| hooks: | ||
| - id: prettier |
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