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Merge pull request #1156 from nf-core/dev
Dev -> master for 3.14.0 release
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‎.github/CONTRIBUTING.md

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@@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from
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## Tests
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You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
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receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
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When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
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Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
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‎.github/PULL_REQUEST_TEMPLATE.md

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@@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnas
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- [ ] If necessary, also make a PR on the nf-core/rnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] Make sure your code lints (`nf-core lint`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.
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- [ ] Output Documentation in `docs/output.md` is updated.
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- [ ] `CHANGELOG.md` is updated.

‎.github/workflows/ci.yml

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- "latest-everything"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1

‎.github/workflows/cloud_tests_full.yml

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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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- 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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"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-gcp:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}
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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@v1
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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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profiles: test_full_gcp
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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_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ 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-azure:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
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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@v1
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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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profiles: test_full_azure
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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_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
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"igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
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"outdir": "${{ 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:

‎.github/workflows/cloud_tests_small.yml

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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@v1
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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-${{ github.sha }}"
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"outdir": "${{ 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-gcp:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
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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@v1
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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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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_GCP }}/rnaseq/results-test-${{ github.sha }}"
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"outdir": "${{ 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-azure:
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if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
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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@v1
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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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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_AZURE }}/rnaseq/results-test-${{ github.sha }}"
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"outdir": "${{ 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:

‎.github/workflows/fix-linting.yml

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runs-on: ubuntu-latest
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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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env:
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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- uses: actions/setup-node@v3
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- uses: actions/setup-node@v4
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- name: Install Prettier
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run: npm install -g prettier @prettier/plugin-php

‎.github/workflows/linting.yml

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EditorConfig:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- uses: actions/setup-node@v3
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- uses: actions/setup-node@v4
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- name: Install editorconfig-checker
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run: npm install -g editorconfig-checker
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Prettier:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- uses: actions/setup-node@v3
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- uses: actions/setup-node@v4
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- name: Install Prettier
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run: npm install -g prettier
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PythonBlack:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Check code lints with Black
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uses: psf/black@stable
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runs-on: ubuntu-latest
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1

‎.github/workflows/release-announcments.yml ‎.github/workflows/release-announcements.yml

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‎.gitpod.yml

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command: |
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pre-commit install --install-hooks
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nextflow self-update
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- name: unset JAVA_TOOL_OPTIONS
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command: |
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unset JAVA_TOOL_OPTIONS
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vscode:
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extensions: # based on nf-core.nf-core-extensionpack
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- codezombiech.gitignore # Language support for .gitignore files

‎CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [[3.14.0](https://github.com/nf-core/rnaseq/releases/tag/3.14.0)] - 2024-01-08
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### Credits
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Special thanks to the following for their contributions to the release:
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- [Adam Talbot](https://github.com/adamrtalbot)
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- [Jonathan Manning](https://github.com/pinin4fjords)
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- [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)
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- [Matthias Zepper](https://github.com/MatthiasZepper)
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- [Maxime Garcia](https://github.com/maxulysse)
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- [Phil Ewels](https://github.com/ewels)
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- [Vlad Savelyev](https://github.com/vladsavelyev)
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Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
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### Enhancements & fixes
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- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling
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- [PR #1141](https://github.com/nf-core/rnaseq/pull/1141) - Important! Template update for nf-core/tools v2.11
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- [PR #1143](https://github.com/nf-core/rnaseq/pull/1143) - Move fasta check back to Groovy ([#1142](https://github.com/nf-core/rnaseq/issues/1142))
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- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners ([#1111](https://github.com/nf-core/rnaseq/issues/1111))
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- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
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- [PR #1150](https://github.com/nf-core/rnaseq/pull/1150) - Be more flexible on attribute values in GTFs ([#1132](https://github.com/nf-core/rnaseq/issues/1132))
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- [PR #1151](https://github.com/nf-core/rnaseq/pull/1151) - fix to #1150: reinstate conditional
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- [PR #1152](https://github.com/nf-core/rnaseq/pull/1152) - Bump container versions for tools using Docker V1 manifest ([#1140](https://github.com/nf-core/rnaseq/issues/1140))
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- [PR #1154](https://github.com/nf-core/rnaseq/pull/1154) - Prerelease 3.14.0 fixes ([#1111](https://github.com/nf-core/rnaseq/issues/1111), [#1153](https://github.com/nf-core/rnaseq/issues/1153))
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- [PR #1157](https://github.com/nf-core/rnaseq/pull/1157) - Add slash to `--outdir` for cloud tests to fix Azure validation issue
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- [PR #1159](https://github.com/nf-core/rnaseq/pull/1159) - Issues loading MultiQC report ([#1158](https://github.com/nf-core/rnaseq/issues/1158))
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### Parameters
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| Old parameter | New parameter |
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| ------------- | ---------------------------- |
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| | `--pseudo_aligner_kmer_size` |
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> **NB:** Parameter has been **updated** if both old and new parameter information is present.
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> **NB:** Parameter has been **added** if just the new parameter information is present.
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> **NB:** Parameter has been **removed** if new parameter information isn't present.
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### Software dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `multiqc` | 1.17 | 1.19 |
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| `qualimap` | 2.2.2d | 2.3 |
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| `rseqc` | 3.0.1 | 5.0.3 |
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> **NB:** Dependency has been **updated** if both old and new version information is present.
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>
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> **NB:** Dependency has been **added** if just the new version information is present.
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>
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> **NB:** Dependency has been **removed** if new version information isn't present.
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## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21
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### Credits

‎README.md

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## Usage
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:::note
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If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
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to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
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with `-profile test` before running the workflow on actual data.
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:::
53+
> [!NOTE]
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> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
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First, prepare a samplesheet with your input data that looks as follows:
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-profile <docker/singularity/.../institute>
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```
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:::warning
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Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
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provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
90-
see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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:::
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> [!WARNING]
85+
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
86+
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).
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‎assets/multiqc_config.yml

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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.13.0" target="_blank">nf-core/rnaseq</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/rnaseq/3.13.0/docs/output" target="_blank">documentation</a>.
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This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/3.14.0" target="_blank">nf-core/rnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/rnaseq/3.14.0/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-rnaseq-methods-description":
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order: -1000
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order: -1002
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export_plots: true
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disable_version_detection: true
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# Run only these modules
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run_modules:

‎bin/dupradar.r

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@@ -93,6 +93,7 @@ curve_y <- curve_y[seq(1, length(curve_y), 10)]
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curve_x = 10^curve_x
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# Write to file
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line="#id: dupradar
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#plot_type: 'linegraph'
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#section_name: 'DupRadar'
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#section_href: 'bioconductor.org/packages/release/bioc/html/dupRadar.html'
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#description: \"provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication.

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