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Merge pull request #1160 from drpatelh/fixes
Final prerelease fixes to fix Cloud CI
2 parents 805c5ac + 36c89c1 commit eb5392a

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‎.github/workflows/cloud_tests_full.yml‎

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@@ -25,12 +25,12 @@ jobs:
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steps:
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- uses: seqeralabs/action-tower-launch@v2
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with:
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revision: ${{ github.sha }}
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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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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@v2
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with:
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revision: ${{ github.sha }}
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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@v2
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with:
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revision: ${{ github.sha }}
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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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@@ -25,6 +25,7 @@ jobs:
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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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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@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@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:

‎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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## v3.14.0 - 2024-01-08
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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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@@ -17,6 +17,8 @@ Special thanks to the following for their contributions to the release:
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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

‎nextflow_schema.json‎

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},
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"min_mapped_reads": {
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"type": "number",
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"default": 5,
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"default": 5.0,
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"fa_icon": "fas fa-percentage",
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"description": "Minimum percentage of uniquely mapped reads below which samples are removed from further processing.",
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"help_text": "Some downstream steps in the pipeline will fail if this threshold is too low."

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