diff --git a/CHANGELOG.md b/CHANGELOG.md
index 048642605eed6e2a07fea840c9a983e7afdbe8a7..d3bd6bd180c5ab2746f058ade9437b196104842f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
version 2.2.0-dev
---------------------------
++ Removed the "installDir" input from CombineVariants.
++ Removed the "extraArgs" input from FilterMutectCalls.
+ Removed unused "verbose" and "quiet" inputs from multiqc.
+ Added parameter_meta sections to a variety of tasks.
+ Picard's BedToIntervalList outputPath input is now optional (with a default of "regions.interval_list")
diff --git a/gatk.wdl b/gatk.wdl
index db9a83333f67acb879dd84df684ca552e1b6b0ba..e0beeb5452e585c51d2f01b47f746ea8945f6ea4 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -407,6 +407,29 @@ task MuTect2 {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ inputBams: {description: "The BAM files on which to perform variant calling.", category: "required"}
+ inputBamsIndex: {description: "The indexes for the input BAM files.", 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.", category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ outputVcf: {description: "The location to write the output VCF file to.", category: "required"}
+ tumorSample: {description: "The name of the tumor/case sample.", category: "required"}
+ normalSample: {description: "The name of the normal/control sample.", category: "common"}
+ germlineResource: {description: "Equivalent to Mutect2's `--germline-resource` option.", category: "advanced"}
+ germlineResourceIndex: {description: "The index for the germline resource.", category: "advanced"}
+ panelOfNormals: {description: "Equivalent to Mutect2's `--panel-of-normals` option.", category: "advanced"}
+ panelOfNormalsIndex: {description: "The index for the panel of normals.", category: "advanced"}
+ f1r2TarGz: {description: "Equivalent to Mutect2's `--f1r2-tar-gz` option.", category: "advanced"}
+ intervals: {description: "Bed files describing the regiosn to operate on.", category: "required"}
+ outputStats: {description: "The location the output statistics should be written to.", 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"}
+ }
}
task LearnReadOrientationModel {
@@ -434,6 +457,15 @@ task LearnReadOrientationModel {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ f1r2TarGz: {description: "A f1r2TarGz file outputed by mutect2.", 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.",
+ 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"}
+ }
}
task MergeStats {
@@ -461,6 +493,15 @@ task MergeStats {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ stats: {description: "Statistics files to be merged.", 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.",
+ 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"}
+ }
}
task GetPileupSummaries {
@@ -496,6 +537,22 @@ task GetPileupSummaries {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ sampleBam: {description: "A BAM file for which a pileup should be created.", category: "required"}
+ sampleBamIndex: {description: "The index of the input BAM file.", category: "required"}
+ variantsForContamination: {description: "A VCF file with common variants.", category: "required"}
+ variantsForContaminationIndex: {description: "The index for the common variants VCF file.", category: "required"}
+ sitesForContamination: {description: "A bed file describing regions to operate on.", category: "required"}
+ sitesForContaminationIndex: {description: "The index for the bed file.", category: "required"}
+ outputPrefix: {description: "The prefix for the ouput.", 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.",
+ 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"}
+ }
}
task CalculateContamination {
@@ -527,6 +584,16 @@ task CalculateContamination {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ tumorPileups: {description: "The pileup summary of a tumor/case sample.", category: "required"}
+ normalPileups: {description: "The pileup summary of the normal/control sample.", category: "common"}
+ 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"}
+ }
}
task FilterMutectCalls {
@@ -542,7 +609,6 @@ task FilterMutectCalls {
File? artifactPriors
Int uniqueAltReadCount = 4
File mutect2Stats
- String? extraArgs
String memory = "24G"
String javaXmx = "12G"
@@ -563,8 +629,7 @@ task FilterMutectCalls {
~{"--unique-alt-read-count " + uniqueAltReadCount} \
~{"-stats " + mutect2Stats} \
--filtering-stats "filtering.stats" \
- --showHidden \
- ~{extraArgs}
+ --showHidden
}
output {
@@ -577,6 +642,26 @@ task FilterMutectCalls {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ 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.", category: "required"}
+ 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"}
+ 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"}
+ uniqueAltReadCount: {description: "Equivalent to FilterMutectCalls' `--unique-alt-read-count` option.", category: "advanced"}
+ mutect2Stats: {description: "Equivalent to FilterMutectCalls' `-stats` option.", 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"}
+ }
}
task SplitNCigarReads {
@@ -636,8 +721,6 @@ task SplitNCigarReads {
task CombineVariants {
input {
- String installDir = "/usr" # .jar location in the docker image
-
File referenceFasta
File referenceFastaFai
File referenceFastaDict
@@ -668,7 +751,7 @@ task CombineVariants {
printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
done
')
- java -Xmx~{javaXmx} -jar ~{installDir}/GenomeAnalysisTK.jar \
+ java -Xmx~{javaXmx} -jar /usr/GenomeAnalysisTK.jar \
-T CombineVariants \
-R ~{referenceFasta} \
--genotypemergeoption ~{genotypeMergeOption} \
@@ -686,4 +769,22 @@ task CombineVariants {
docker: dockerImage
memory: memory
}
+
+ parameter_meta {
+ 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.", category: "required"}
+ referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+ genotypeMergeOption: {description: "Equivalent to CombineVariants' `--genotypemergeoption` option.", category: "advanced"}
+ filteredRecordsMergeType: {description: "Equivalent to CombineVariants' `--filteredrecordsmergetype` option.", category: "advanced"}
+ identifiers: {description: "The sample identifiers in the same order as variantVcfs.", category: "required"}
+ variantVcfs: {description: "The input VCF files in the same order as identifiers.", category: "required"}
+ variantIndexes: {description: "The indexes of the input VCF files.", category: "required"}
+ outputPath: {description: "The location the output 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.",
+ 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"}
+ }
}