Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage #1981
Workflow file for this run
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| 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] | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Hash Github Workspace | |
| id: hash_workspace | |
| run: | | |
| echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
| - name: Cache test data | |
| id: cache-testdata | |
| uses: actions/cache@v3 | |
| with: | |
| path: test-datasets/ | |
| key: ${{ steps.hash_workspace.outputs.digest }} | |
| - name: Check out test data | |
| if: steps.cache-testdata.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: nf-core/test-datasets | |
| ref: rnaseq3 | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| run: | | |
| for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ | |
| star_salmon: | |
| name: Test STAR Salmon with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| - "--skip_trimming" | |
| - "--gtf false" | |
| - "--star_index false" | |
| - "--transcript_fasta false" | |
| - "--min_mapped_reads 90" | |
| - "--with_umi" | |
| - "--with_umi --skip_trimming" | |
| - "--remove_ribo_rna --skip_qualimap" | |
| - "--bam_csi_index" | |
| - "--save_align_intermeds --save_reference" | |
| - "--featurecounts_group_type false" | |
| - "--trimmer fastp" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Hash Github Workspace | |
| id: hash_workspace | |
| run: | | |
| echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
| - name: Cache test data | |
| id: cache-testdata | |
| uses: actions/cache@v3 | |
| with: | |
| path: test-datasets/ | |
| key: ${{ steps.hash_workspace.outputs.digest }} | |
| - name: Check out test data | |
| if: steps.cache-testdata.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: nf-core/test-datasets | |
| ref: rnaseq3 | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| run: | | |
| for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with STAR and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ | |
| star_rsem: | |
| name: Test STAR RSEM with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| - "--rsem_index false" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Hash Github Workspace | |
| id: hash_workspace | |
| run: | | |
| echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
| - name: Cache test data | |
| id: cache-testdata | |
| uses: actions/cache@v3 | |
| with: | |
| path: test-datasets/ | |
| key: ${{ steps.hash_workspace.outputs.digest }} | |
| - name: Check out test data | |
| if: steps.cache-testdata.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: nf-core/test-datasets | |
| ref: rnaseq3 | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| run: | | |
| for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with RSEM STAR and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ | |
| hisat2: | |
| name: Test HISAT2 with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| - "--hisat2_index false" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Hash Github Workspace | |
| id: hash_workspace | |
| run: | | |
| echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
| - name: Cache test data | |
| id: cache-testdata | |
| uses: actions/cache@v3 | |
| with: | |
| path: test-datasets/ | |
| key: ${{ steps.hash_workspace.outputs.digest }} | |
| - name: Check out test data | |
| if: steps.cache-testdata.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: nf-core/test-datasets | |
| ref: rnaseq3 | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| run: | | |
| for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with HISAT2 and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ | |
| pseudo: | |
| name: Test Pseudoaligners with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--pseudo_aligner salmon --skip_qc" | |
| - "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment" | |
| - "--pseudo_aligner salmon --salmon_index false --transcript_fasta false" | |
| - "--pseudo_aligner kallisto --skip_qc" | |
| - "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment" | |
| - "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Hash Github Workspace | |
| id: hash_workspace | |
| run: | | |
| echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
| - name: Cache test data | |
| id: cache-testdata | |
| uses: actions/cache@v3 | |
| with: | |
| path: test-datasets/ | |
| key: ${{ steps.hash_workspace.outputs.digest }} | |
| - name: Check out test data | |
| if: steps.cache-testdata.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: nf-core/test-datasets | |
| ref: rnaseq3 | |
| path: test-datasets/ | |
| - name: Replace remote paths in samplesheets | |
| run: | | |
| for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
| sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
| echo "========== $f ============" | |
| cat $f | |
| echo "========================================" | |
| done; | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with Salmon or Kallisto and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ |