diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index abb541fc..ff7dee1e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,12 +31,12 @@ jobs: strategy: matrix: # Nextflow versions: check pipeline minimum and current latest - nxf_ver: ['22.10.1', '23.04.1'] + nxf_ver: ['22.10.1', '24.04.2'] steps: - name: Check out pipeline code - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Cache Nextflow binary - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-nextflow with: path: /usr/local/bin/nextflow @@ -49,7 +49,7 @@ jobs: wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - name: Cache seqtk binary - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-seqtk with: path: /usr/local/bin/seqtk @@ -63,7 +63,7 @@ jobs: make install which seqtk - name: Cache subsampled influenza.fna - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-influenza-fna with: path: influenza-10k.fna.zst @@ -73,7 +73,7 @@ jobs: run: | curl --silent -SLk ${FASTA_ZST_URL} | zstdcat | seqtk sample -s 789 - 10000 | zstd -ck > influenza-10k.fna.zst - name: Cache influenza.csv - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-influenza-csv with: path: influenza.csv.zst @@ -90,12 +90,12 @@ jobs: --ncbi_influenza_metadata influenza.csv.zst - name: Upload Artifact if: success() - uses: actions/upload-artifact@v1.0.0 + uses: actions/upload-artifact@v4 with: name: illumina-test-results-${{ matrix.nxf_ver }} path: results/pipeline_info - name: Upload .nextflow.log - uses: actions/upload-artifact@v1.0.0 + uses: actions/upload-artifact@v4 with: name: nextflow-log-illumina-${{ matrix.nxf_ver }} path: .nextflow.log @@ -111,12 +111,12 @@ jobs: strategy: matrix: # Nextflow versions: check pipeline minimum and current latest - nxf_ver: ['22.10.1', '23.04.1'] + nxf_ver: ['22.10.1', '24.04.2'] steps: - name: Check out pipeline code - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Cache Nextflow binary - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-nextflow with: path: /usr/local/bin/nextflow @@ -129,7 +129,7 @@ jobs: wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - name: Cache seqtk binary - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-seqtk with: path: /usr/local/bin/seqtk @@ -143,7 +143,7 @@ jobs: make install which seqtk - name: Cache test sample reads - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-reads with: path: reads/ @@ -177,7 +177,7 @@ jobs: echo "ntc-bc31,$(realpath reads/ntc-bc31.fastq.gz)" | tee -a samplesheet.csv echo "ntc-bc47,$(realpath reads/ntc-bc47.fastq.gz)" | tee -a samplesheet.csv - name: Cache subsampled influenza.fna - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-influenza-fna with: path: influenza-10k.fna.zst @@ -187,7 +187,7 @@ jobs: run: | curl --silent -SLk ${FASTA_ZST_URL} | zstdcat | seqtk sample -s 789 - 10000 | zstd -ck > influenza-10k.fna.zst - name: Cache influenza.csv - uses: actions/cache@v3 + uses: actions/cache@v4 id: cache-influenza-csv with: path: influenza.csv.zst @@ -207,25 +207,25 @@ jobs: - name: Tree of results run: tree -h results/ - name: Upload .nextflow.log - uses: actions/upload-artifact@v1.0.0 + uses: actions/upload-artifact@v4 with: name: nextflow-log-nanopore-${{ matrix.nxf_ver }} path: .nextflow.log - name: Upload pipeline_info/ if: success() - uses: actions/upload-artifact@v1.0.0 + uses: actions/upload-artifact@v4 with: name: nanopore-test-results-pipline_info-${{ matrix.nxf_ver }} path: results/pipeline_info - name: Upload nf-flu-subtyping-report.xlsx if: success() - uses: actions/upload-artifact@v1.0.0 + uses: actions/upload-artifact@v4 with: name: nanopore-test-results-subtyping-report-${{ matrix.nxf_ver }} path: results/nf-flu-subtyping-report.xlsx - name: Upload multiqc_report.html if: success() - uses: actions/upload-artifact@v1.0.0 + uses: actions/upload-artifact@v4 with: name: nanopore-test-results-multiqc-${{ matrix.nxf_ver }} path: results/MultiQC/multiqc_report.html diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 2e297aad..a9ac23c2 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,10 +11,8 @@ jobs: Markdown: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '18' + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 - name: Install markdownlint run: npm install -g markdownlint-cli - name: Run Markdownlint @@ -49,10 +47,8 @@ jobs: YAML: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 - - uses: actions/setup-node@v1 - with: - node-version: '18' + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 - name: Install yaml-lint run: npm install -g yaml-lint - name: Run yaml-lint diff --git a/CHANGELOG.md b/CHANGELOG.md index cd63bf4b..84ff508d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,10 @@ Long overdue software updates release. * multiqc: `1.12` -> `1.21` * seqtk: `1.3` -> `1.4` +### Changes + +* dev: update GitHub Actions versions for CI and linting workflows + ## [[3.3.8](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.3.8)] - 2024-02-16 This bugfix patch release fixes an issue where a large number of ambiguous bases in the IRMA consensus can hinder