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Merge branch 'dev' into nf-core-template-merge-2.11
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‎.github/workflows/awsfulltest.yml‎

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‎.github/workflows/awstest.yml‎

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‎.github/workflows/ci.yml‎

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@@ -35,9 +35,254 @@ jobs:
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with:
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version: "${{ matrix.NXF_VER }}"
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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with:
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repository: nf-core/test-datasets
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ref: rnaseq3
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path: test-datasets/
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- name: Replace remote paths in samplesheets
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run: |
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for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
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done;
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- name: Run pipeline with test data
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# TODO nf-core: You can customise CI pipeline run tests as required
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# For example: adding multiple test runs with different parameters
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# Remember that you can parallelise this by using strategy.matrix
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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star_salmon:
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name: Test STAR Salmon with workflow parameters
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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parameters:
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- "--skip_qc"
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- "--skip_trimming"
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- "--gtf false"
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- "--star_index false"
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- "--transcript_fasta false"
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- "--min_mapped_reads 90"
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- "--with_umi"
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- "--with_umi --skip_trimming"
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- "--remove_ribo_rna --skip_qualimap"
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- "--bam_csi_index"
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- "--save_align_intermeds --save_reference"
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- "--featurecounts_group_type false"
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- "--trimmer fastp"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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with:
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repository: nf-core/test-datasets
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ref: rnaseq3
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path: test-datasets/
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- name: Replace remote paths in samplesheets
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run: |
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for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
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done;
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with STAR and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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star_rsem:
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name: Test STAR RSEM with workflow parameters
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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parameters:
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- "--skip_qc"
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- "--rsem_index false"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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with:
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repository: nf-core/test-datasets
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ref: rnaseq3
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path: test-datasets/
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- name: Replace remote paths in samplesheets
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run: |
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for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
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done;
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with RSEM STAR and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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hisat2:
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name: Test HISAT2 with workflow parameters
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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parameters:
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- "--skip_qc"
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- "--hisat2_index false"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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with:
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repository: nf-core/test-datasets
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ref: rnaseq3
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path: test-datasets/
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- name: Replace remote paths in samplesheets
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run: |
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for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
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done;
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with HISAT2 and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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pseudo:
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name: Test Pseudoaligners with workflow parameters
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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parameters:
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- "--pseudo_aligner salmon --skip_qc"
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- "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
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- "--pseudo_aligner salmon --salmon_index false --transcript_fasta false"
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- "--pseudo_aligner kallisto --skip_qc"
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- "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
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- "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
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uses: actions/checkout@v3
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with:
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repository: nf-core/test-datasets
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ref: rnaseq3
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path: test-datasets/
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- name: Replace remote paths in samplesheets
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run: |
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for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
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done;
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with Salmon or Kallisto and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

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