Commit 8d7527db authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'vep_docfix' into 'develop'

add more info to VepNormalizer tool help


See merge request !157
parents 97eb9752 33a52ed7
......@@ -239,25 +239,24 @@ object VepNormalizer extends ToolCommand {
c.copy(inputVCF = x)
} validate {
x => if (x.exists) success else failure("Input VCF not found")
} text "Input VCF file"
} text "Input VCF file. Required."
opt[File]('O', "OutputFile") required () valueName "<vcf>" action { (x, c) =>
c.copy(outputVCF = x)
} validate {
x =>
if (!x.getName.endsWith(".vcf") && (!x.getName.endsWith(".vcf.gz")) && (!x.getName.endsWith(".bcf")))
failure("Unsupported output file type") else success
} text "Output VCF file"
} text "Output VCF file. Required."
opt[String]('m', "mode") required () valueName "<mode>" action { (x, c) =>
c.copy(mode = x)
} validate {
x => if (x == "explode") success else if (x == "standard") success else failure("Unsupported mode")
} text "Mode"
} text "Mode. Can choose between <standard> (generates standard vcf) and <explode> (generates new record for each transcript). Required."
opt[Unit]("do-not-remove") action { (x, c) =>
c.copy(removeCSQ = false)
} text "Do not remove CSQ tag"
} text "Do not remove CSQ tag. Optional"
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