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drpatelhdrpatelh
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Fix merge conflicts
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‎.github/workflows/awsfulltest.yml‎

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -12,20 +12,22 @@ jobs:
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name: Run AWS full tests
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if: github.repository == 'nf-core/rnaseq'
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runs-on: ubuntu-latest
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# Do a full-scale run with each of the three aligners
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strategy:
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matrix:
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aligner: ["star_salmon", "star_rsem", "hisat2"]
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steps:
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- name: Launch workflow via tower
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uses: nf-core/tower-action@v3
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# TODO nf-core: You can customise AWS full pipeline tests as required
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# Add full size test data (but still relatively small datasets for few samples)
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# on the `test_full.config` test runs with only one set of parameters
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
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workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnaseq/work-${{ github.sha }}
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parameters: |
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{
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ github.sha }}"
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"outdir" : "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
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"aligner": "${{ matrix.aligner }}"
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}
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profiles: test_full,aws_tower
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- uses: actions/upload-artifact@v3

‎.github/workflows/ci.yml‎

Lines changed: 98 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -36,8 +36,103 @@ jobs:
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version: "${{ matrix.NXF_VER }}"
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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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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') }}
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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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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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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,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
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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') }}
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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: 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,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
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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') }}
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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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109+
- 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,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
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salmon:
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name: Test Salmon with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
121+
runs-on: ubuntu-latest
122+
strategy:
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matrix:
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parameters:
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- "--skip_qc --skip_alignment"
126+
- "--salmon_index false --transcript_fasta false"
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steps:
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- name: Check out pipeline code
129+
uses: actions/checkout@v2
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131+
- name: Install Nextflow
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run: |
133+
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 and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results

‎.nf-core.yml‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1 +1,6 @@
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repository_type: pipeline
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lint:
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files_unchanged:
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- assets/email_template.html
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- assets/email_template.txt
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- lib/NfcoreTemplate.groovy

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