diff --git a/gatk.wdl b/gatk.wdl index e0beeb5452e585c51d2f01b47f746ea8945f6ea4..5ca149c335ece5cc6edcfb45ecde6def36cacdf3 100644 --- a/gatk.wdl +++ b/gatk.wdl @@ -114,7 +114,7 @@ task BaseRecalibrator { inputBamIndex: {description: "The index of the input BAM file.", category: "required"} recalibrationReportPath: {description: "The location to write the BQSR report to.", category: "required"} sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"} - knownIndelsSitesVCFs: {description: "VCf files with known indels.", category: "advanced"} + knownIndelsSitesVCFs: {description: "VCF files with known indels.", category: "advanced"} knownIndelsSitesVCFIndexes: {description: "The indexed for the known variant VCFs.", category: "advanced"} dbsnpVCF: {description: "A dbSNP VCF.", category: "common"} dbsnpVCFIndex: {description: "The index for the dbSNP VCF.", category: "common"} @@ -275,7 +275,7 @@ task GenotypeGVCFs { gvcfFiles: {description: "The GVCF files to be genotypes.", category: "required"} gvcfFilesIndex: {description: "The index of the input GVCF files.", category: "required"} intervals: {description: "Bed files or interval lists describing the regions to operate on.", category: "required"} - outputPath: {description: "The location to write the output VCf file to.", category: "required"} + outputPath: {description: "The location to write the output VCF file to.", category: "required"} referenceFasta: {description: "The reference fasta file which was also used for mapping.", category: "required"} referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", @@ -649,7 +649,7 @@ task FilterMutectCalls { referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"} unfilteredVcf: {description: "An unfiltered VCF file as produced by Mutect2.", category: "required"} unfilteredVcfIndex: {description: "The index of the unfiltered VCF file.", category: "required"} - outputVcf: {description: "The location the filtered VCf file should be written.", category: "required"} + outputVcf: {description: "The location the filtered VCF file should be written.", category: "required"} contaminationTable: {description: "Equivalent to FilterMutectCalls' `--contamination-table` option.", category: "advanced"} mafTumorSegments: {description: "Equivalent to FilterMutectCalls' `--tumor-segmentation` option.", category: "advanced"} artifactPriors: {description: "Equivalent to FilterMutectCalls' `--ob-priors` option.", category: "advanced"} diff --git a/picard.wdl b/picard.wdl index f1f0772354460e50c60bc2491cda9c9ff593b90e..48ebf2d5c0e5d0dbf4e7d60d3be563498161e328 100644 --- a/picard.wdl +++ b/picard.wdl @@ -483,7 +483,7 @@ task MergeVCFs { parameter_meta { inputVCFs: {description: "The VCF files to be merged.", category: "required"} inputVCFsIndexes: {description: "The indexes of the VCF files.", category: "required"} - outputVcfPath: {description: "The location the output VCf file should be written to.", category: "required"} + outputVcfPath: {description: "The location the output VCF file should be written to.", category: "required"} 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.",