Panel of Normals #24
Panel of Normals #24
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Conflicts: docs/output.md main.nf
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You need to include the EDIT: Done except for |
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And if you could add some docs about the PONs that would be very nice as well |
maxulysse
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enhancement
docs/output.md
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| * `MuTect2_[TUMORSAMPLE]_vs_[NORMALSAMPLE].vcf.gz` and `MuTect2_[TUMORSAMPLE]_vs_[NORMALSAMPLE].vcf.gz.tbi` | ||
| * `Mutect2_[TUMORSAMPLE]_vs_[NORMALSAMPLE].vcf.gz` and `Mutect2_[TUMORSAMPLE]_vs_[NORMALSAMPLE].vcf.gz.tbi` |
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Can you describe the new organisation of files here?
docs/output.md
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| For further reading and documentation see the [MuTect2 manual](https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.2.0/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php). | ||
| For further reading and documentation see the [Mutect2 manual](https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.2.0/org_broadinstitute_hellbender_tools_walkers_mutect_Mutect2.php). |
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Can you put some lines about PON, maybe add also the comment that's in the main.nf script:
please make a panel-of-normals, using at least 40 samples
https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2
| publishDir "${params.outdir}/VariantCalling/${idSampleTumor}_vs_${idSampleNormal}/Mutect2", mode: params.publishDirMode | ||
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| input: | ||
| set caller, |
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I don't think you have caller here in this channel.
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You could also group the two sets into just one with another groupTuple
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Now there is the missing caller - I would prefer to leave it it as it is as there is a fork later and it is already pretty cluttered.
| tag {idSampleTumor + "_vs_" + idSampleNormal + "_" + intervalBed.baseName } | ||
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| input: | ||
| set idPatient, idSampleNormal, file(bamNormal), file(baiNormal), idSampleTumor, file(bamTumor), file(baiTumor), file(intervalBed) from pairBamPileupSummaries |
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I don't think bamNormal is needed in this process.
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That is true, but simpler now to multiply the channels for variant callers. We can dissect the channel and re-assemble if you feel it is bad style.
Conflicts: CHANGELOG.md main.nf
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The error handling code is buggy still (from the current template version unfortunately): if (workflow.stats.ignoredCount > 0 && workflow.success) {
log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}"
log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}"
}Is the way to do it - can do it via an own PR ... |
Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
Panel of normals (PON) is needed to filter GATK4 Mutect2 somatic calls, though also useful to annotate somatic calls produced by other software also. This PR focuses on Mutect2, and follows instructions at https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2
PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updated