From 85717efec10b69255bd99dc49973fcf229215929 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 13 Jan 2020 16:26:09 +0100
Subject: [PATCH] add parameter_meta to vardict
---
vardict.wdl | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/vardict.wdl b/vardict.wdl
index 85e5fd2..ed9ee22 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -69,4 +69,34 @@ task VarDict {
memory: memory
docker: dockerImage
}
+
+ parameter_meta {
+ tumorSampleName: {description: "The name of the tumor/case sample.", category: "required"}
+ tumorBam: {description: "The tumor/case sample's BAM file.", category: "required"}
+ tumorBamIndex: {description: "The index for the tumor/case sample's BAM file.", category: "required"}
+ normalSampleName: {description: "The name of the normal/control sample.", category: "common"}
+ normalBam: {description: "The normal/control sample's BAM file.", category: "common"}
+ normalBamIndex: {description: "The normal/control sample's BAM file.", category: "common"}
+ referenceFasta: {description: "The reference fasta file.", category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ bedFile: {description: "A bed file describing the regions to operate on. These regions must be below 1e6 bases in size.", category: "required"}
+ outputVcf: {description: "The location to write the output VCF file to.", category: "required"}
+ chromosomeColumn: {description: "Equivalent to vardict-java's `-c` option.", category: "advanced"}
+ startColumn: {description: "Equivalent to vardict-java's `-S` option.", category: "advanced"}
+ endColumn: {description: "Equivalent to vardict-java's `-E` option.", category: "advanced"}
+ geneColumn: {description: "Equivalent to vardict-java's `-g` option.", category: "advanced"}
+ outputCandidateSomaticOnly: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-M` flag.", category: "advanced"}
+ outputAllVariantsAtSamePosition: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-A` flag.", category: "advanced"}
+ mappingQuality: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-Q` option.", category: "advanced"}
+ minimumTotalDepth: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-d` option.", category: "advanced"}
+ minimumVariantDepth: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-v` option.", category: "advanced"}
+ minimumAlleleFrequency: {description: "Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-f` option.", category: "advanced"}
+
+ threads: {description: "The number of threads to use.", category: "advanced"}
+ memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
+ category: "advanced"}
+ dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"}
+ }
}
--
GitLab