Add GATK contamination check to complement VerifyBamID2#758
Add GATK contamination check to complement VerifyBamID2#758dorotejavujinovic wants to merge 14 commits into
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- Add CONTAMINATION_CHECK subworkflow using GATK4 - Add PARSE_CONTAMINATION module for MultiQC integration - Add GATK4 GetPileupSummaries and CalculateContamination modules - Implement conditional intervals handling (WGS vs WES) - Update workflow to integrate contamination check after QC_BAM - Configure MultiQC to display contamination results
Updated GATK contamination configuration for clarity and consistency.
Introduced GATK contamination check for WES/WGS samples, added new parameters and subworkflow, and updated MultiQC configuration.
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Thanks for the PR @dorotejavujinovic!
| ext.prefix = { "${meta.id}_sorted_md" } | ||
| publishDir = [ | ||
| enabled: !params.save_mapped_as_cram, | ||
| enabled: true, |
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I am curious why do you want to change this?
| withName: '.*ALIGN:ALIGN_BWA_BWAMEM2_BWAMEME:SAMTOOLS_INDEX_MARKDUP' { | ||
| publishDir = [ | ||
| enabled: !params.save_mapped_as_cram, | ||
| enabled: true, |
| script: | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| #!/usr/bin/env python3 |
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Can you make this a module binary? We have had issues in the past with some systems interpreting indents differently.
| v.write('"${task.process}":\\n') | ||
| v.write(' python: "3.11"\\n') | ||
| """ | ||
| } |
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Also can you add a stub section?
| ### Added | ||
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| - Added GATK contamination check for WES/WGS samples as complement to VerifyBamID2 | ||
| - New parameters: `run_contamination`, `contamination_sites`, `contamination_sites_tbi` | ||
| - CONTAMINATION_CHECK subworkflow using GATK4 GetPileupSummaries and CalculateContamination | ||
| - PARSE_CONTAMINATION module for MultiQC integration | ||
| - Contamination results displayed in MultiQC with color-coded thresholds |
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You can add your log entries to 2.7.0dev since its the one in development. And don't forget to link the PR to your entries ;)
Also, we have a separate table for parameters and new tools under the ##Fixed section of 2.7.0dev, so you can add that information there.
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Could you add a test for this subworkflow? We are currently in the process of adding subworkflow level tests using nf-test, so it would be fantastic if you can include one for this subworkflow.
…f-tests - Convert parse_contamination inline Python to module binary (bin/) - Add stub section to parse_contamination module - Move CHANGELOG entries into 2.7.0dev section with PR links and tables - Revert unrelated publishDir changes in align config - Add nf-test subworkflow tests for contamination_check (WGS + WES)
Missing closing brace and installed_by field caused nf-core lint to crash with TypeError during dependency recreation.
Update git_sha to ae8cd884f895 which matches the actual installed module versions (GATK 4.6.2.0 with nf-core code style updates).
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PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedDescription
Adds GATK-based contamination detection to complement VerifyBamID2.
Background
Implementation
CONTAMINATION_CHECKusing GATK4 GetPileupSummaries and CalculateContaminationPARSE_CONTAMINATIONfor MultiQC integrationUsage
Testing
Tested on both WGS and WES samples with successful integration into MultiQC reports.