diff --git a/vardict.wdl b/vardict.wdl index 85e5fd2baf38c29a48e16cc06aa5b4c5ae1d495f..ed9ee22ddbc6595d7ff4dcf3d16c23e0cb0308e0 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"} + } }