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PON not correctly validated #648

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Merged
maxulysse merged 3 commits into from
Jul 18, 2022
Merged

PON not correctly validated #648

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85afefc
add warn if intervals is provided without wes
FriederikeHanssen Jul 17, 2022
62e182e
combine conditionals
FriederikeHanssen Jul 17, 2022
1411796
fix pon validation
FriederikeHanssen Jul 17, 2022
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3 changes: 0 additions & 3 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -62,9 +62,6 @@ params {
cf_mincov = 0 // ControlFreec default values
cf_minqual = 0 // ControlFreec default values
cf_window = null // by default we are not using this in Control-FREEC

pon = null // No default PON (Panel of Normals) file for GATK Mutect2
pon_tbi = null // No default PON index for GATK Mutect2
ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2
wes = false // Set to true, if data is exome/targeted sequencing data. Used to use correct models in various variant callers
joint_germline = false // g.vcf & joint germline calling are not run by default if HaplotypeCaller is selected
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4 changes: 3 additions & 1 deletion workflows/sarek.nf
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Expand Up @@ -56,8 +56,10 @@ ch_input_sample = extract_csv(file(params.input, checkIfExists: true))

// Fails when wrongfull extension for intervals file
if (params.wes && !params.step == 'annotate') {
if (params.intervals && !params.intervals.endsWith("bed")) exit 1, "Target file specified with `--intervals` must be in BED format"
if (params.intervals && !params.intervals.endsWith("bed")) exit 1, "Target file specified with `--intervals` must be in BED format for targeted data"
} else {
log.warn("Interval file was provided without parameter `--wes`: Pipeline will assume this is Whole-genome-sequencing data.")

if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("interval_list")) exit 1, "Interval file must end with .bed or .interval_list"
}

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