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Merge branch 'dev' into nf-core-template-merge-3.3.1
2 parents 949f8fc + 21acf5a commit ca7d3b6

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‎.github/include.yaml‎

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".":
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- ./.github/workflows/**
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- ./nf-test.config
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- ./nextflow.config
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tests:
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- ./assets/*
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- ./bin/*
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- ./conf/*
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- ./main.nf
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- ./nextflow_schema.json

‎.github/workflows/awsfulltest.yml‎

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# run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
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if: github.repository == 'nf-core/rnaseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch' || github.event_name == 'release'
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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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- name: Set revision variable
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id: revision
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"aligner": "${{ matrix.aligner }}",
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"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnaseq/results-${{ steps.revision.outputs.revision }}"
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}
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profiles: test_full

‎.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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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' || !github.event.inputs }}
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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@v2
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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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revision: ${{ github.sha }}
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profiles: test_full_aws
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"aligner": "${{ matrix.aligner }}",
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"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
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}
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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-azure:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
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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@v2
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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: ${{ secrets.TOWER_CE_AZURE_CPU }}
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workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
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run_name: "azure_rnaseq_full_${{ matrix.aligner }}"
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revision: ${{ github.sha }}
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profiles: test_full_azure
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"aligner": "${{ matrix.aligner }}",
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"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/",
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"igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
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}
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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 == 'gcp' || !github.event.inputs }}
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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@v2
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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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revision: ${{ github.sha }}
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profiles: test_full_gcp
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
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"aligner": "${{ matrix.aligner }}",
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"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}/"
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}
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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

‎.github/workflows/cloud_tests_small.yml‎

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name: small-sized tests on cloud providers
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run-name: Submitting workflow to all cloud providers using small sized data
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on:
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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-small-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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steps:
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- uses: seqeralabs/action-tower-launch@v2
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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_small"
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revision: ${{ github.sha }}
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profiles: test
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parameters: |
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{
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"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}/"
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}
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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-small-tests-on-azure:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
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runs-on: ubuntu-latest
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steps:
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- uses: seqeralabs/action-tower-launch@v2
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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: ${{ secrets.TOWER_CE_AZURE_CPU }}
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workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
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run_name: "azure_rnaseq_small"
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revision: ${{ github.sha }}
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profiles: test
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parameters: |
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{
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"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}/"
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}
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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-small-tests-on-gcp:
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if: ${{ github.event.inputs.platform == 'gcp' }}
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runs-on: ubuntu-latest
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steps:
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- uses: seqeralabs/action-tower-launch@v2
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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_small"
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revision: ${{ github.sha }}
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profiles: test
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parameters: |
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{
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"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}/"
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}
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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

‎.gitignore‎

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*.pyc
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.DS_Store
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.nextflow*
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work/
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.nf-test.log
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data/
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nf-test
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.nf-test*
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results/
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.DS_Store
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testing/
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test.xml
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testing*
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*.pyc
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testing/
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work/
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null/

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