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Add VCF QC #522

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merged 12 commits into from
Apr 21, 2022
Merged

Add VCF QC #522

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4c78bd0
add vcf vc workflow
FriederikeHanssen Apr 19, 2022
e5995cf
Suggestion for how to deal with multi tools for annotation and qc
FriederikeHanssen Apr 19, 2022
9413cff
add tool naming to meta-map for all callers
FriederikeHanssen Apr 19, 2022
2ceb02c
add tool for annotation to annotate multiple tools for the same sample
FriederikeHanssen Apr 19, 2022
88a25d8
Add multiqc
FriederikeHanssen Apr 19, 2022
8f69345
tampering with the config
FriederikeHanssen Apr 19, 2022
c183f1e
remove comments
FriederikeHanssen Apr 19, 2022
dad599e
Fix trimgalore used output
FriederikeHanssen Apr 20, 2022
d6eaa44
Fix BQSR output for reporting
FriederikeHanssen Apr 20, 2022
daffd96
Add snpeff file size as recommended in multiQC issue 229
FriederikeHanssen Apr 21, 2022
c034f5f
Finish configuration for MQC
FriederikeHanssen Apr 21, 2022
25ded7d
Fix fastqc output path
FriederikeHanssen Apr 21, 2022
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31 changes: 31 additions & 0 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -903,6 +903,37 @@ process{
ext.prefix = {"${meta.id}.somatic_snvs"}
}

// VCF QC
withName: 'BCFTOOLS_STATS'{
ext.when = { !(params.skip_tools && params.skip_tools.contains('bcftools')) }
ext.prefix = { "${meta.variantcaller}_${vcf.baseName.minus(".vcf")}" }
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publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/bcftools" },
]
}
//"${meta.id}".concat('.').concat(reads.get(0).name.findAll(/part_([0-9]+)?/).last())

withName: 'VCFTOOLS_.*'{
ext.when = { !(params.skip_tools && params.skip_tools.contains('vcftools')) }
ext.prefix = { "${vcf.baseName}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/vcftools" },
]
}

withName: 'VCFTOOLS_TSTV_COUNT'{
ext.args = "--TsTv-by-count"
}

withName: 'VCFTOOLS_TSTV_QUAL'{
ext.args = "--TsTv-by-qual"
}

withName: 'VCFTOOLS_SUMMARY'{
ext.args = "--FILTER-summary"
}
}

//withName: 'GENOMICSDBIMPORT' {
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7 changes: 6 additions & 1 deletion subworkflows/nf-core/variantcalling/strelka/single/main.nf
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27 changes: 27 additions & 0 deletions subworkflows/nf-core/vcf_qc.nf
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7 changes: 6 additions & 1 deletion workflows/sarek.nf
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Expand Up @@ -183,6 +183,8 @@ include { TUMOR_ONLY_VARIANT_CALLING } from '../subworkflows
// Variant calling on tumor/normal pair
include { PAIR_VARIANT_CALLING } from '../subworkflows/local/pair_variant_calling'

include { VCF_QC } from '../subworkflows/nf-core/vcf_qc'

// Annotation
include { ANNOTATE } from '../subworkflows/local/annotate'

Expand Down Expand Up @@ -673,7 +675,7 @@ workflow SAREK {
chr_files,
mappability)

// Gather vcf files for annotation
// Gather vcf files for annotation and QC
vcf_to_annotate = Channel.empty()
vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.deepvariant_vcf)
vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.freebayes_vcf)
Expand All @@ -693,6 +695,9 @@ workflow SAREK {
ch_versions = ch_versions.mix(PAIR_VARIANT_CALLING.out.versions)
ch_versions = ch_versions.mix(TUMOR_ONLY_VARIANT_CALLING.out.versions)

//QC
VCF_QC(vcf_to_annotate, intervals_bed_combined)

// ANNOTATE
if (params.step == 'annotate') vcf_to_annotate = ch_input_sample

Expand Down