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Merge pull request #966 from nf-core/dev
Dev -> Master for 3.11 release
2 parents 6e1e448 + fbffe86 commit 48fb9b4

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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 +35,33 @@ jobs:
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with:
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version: "${{ matrix.NXF_VER }}"
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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: rnaseq3_10-test-data
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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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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
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nextflow run ${GITHUB_WORKSPACE} -profile test,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
@@ -58,18 +82,43 @@ jobs:
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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: 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: rnaseq3_10-test-data
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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,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
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nextflow run ${GITHUB_WORKSPACE} -profile test,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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- name: Check out pipeline code
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uses: actions/checkout@v2
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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: rnaseq3_10-test-data
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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,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
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nextflow run ${GITHUB_WORKSPACE} -profile test,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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- name: Check out pipeline code
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uses: actions/checkout@v2
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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: rnaseq3_10-test-data
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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,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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salmon:
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name: Test Salmon with workflow parameters
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- name: Check out pipeline code
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uses: actions/checkout@v2
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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: rnaseq3_10-test-data
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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: |
245+
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 "========================================"
250+
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 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
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

‎.github/workflows/cloud_tests_full.yml‎

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name: full-sized tests on cloud providers
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run-name: Submitting workflow to all cloud providers using full sized data
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on:
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release:
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types: [published]
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workflow_dispatch:
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inputs:
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platform:
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description: "Platform to run test"
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required: true
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default: "all"
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type: choice
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options:
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- all
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- aws
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- azure
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- gcp
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jobs:
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run-full-tests-on-aws:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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aligner: ["star_salmon", "star_rsem"]
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steps:
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- uses: seqeralabs/action-tower-launch@v1
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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: ${{ secrets.TOWER_CE_AWS_CPU }}
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workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
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run_name: "aws_rnaseq_full_${{ matrix.aligner }}"
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profiles: test_full_aws
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
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}
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wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
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path: tower_action_*.log
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run-full-tests-on-gcp:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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aligner: ["star_salmon", "star_rsem"]
50+
steps:
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- uses: seqeralabs/action-tower-launch@v1
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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: ${{ secrets.TOWER_CE_GCP_CPU }}
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workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
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run_name: "gcp_rnaseq_full_${{ matrix.aligner }}"
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profiles: test_full_gcp
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
63+
}
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wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
68+
path: tower_action_*.log
69+
run-full-tests-on-azure:
70+
if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
71+
runs-on: ubuntu-latest
72+
strategy:
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matrix:
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aligner: ["star_salmon", "star_rsem"]
75+
steps:
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- uses: seqeralabs/action-tower-launch@v1
77+
with:
78+
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
79+
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
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compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
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workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
82+
run_name: "azure_rnaseq_full_${{ matrix.aligner }}"
83+
profiles: test_full_azure
84+
parameters: |
85+
{
86+
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
87+
"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
88+
"igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
89+
}
90+
wait: false
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- uses: actions/upload-artifact@v3
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with:
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name: Tower debug log file
94+
path: tower_action_*.log

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