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Commit 0b2a14fc authored by Cats's avatar Cats
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add parameter_meta to BaseRecibrator

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gatk.wdl
+ 24
− 2
View file @ 0b2a14fc
......@@ -51,7 +51,7 @@ task ApplyBQSR {
inputBamIndex: {description: "The input BAM file's index.", category: "required"}
outputBamPath: {description: "The location the resulting BAM file should be written.", category: "required"}
recalibrationReport: {description: "The BQSR report the be used for recalibration.", category: "required"}
sequenceGroupInterval: {description: "The regions to operate on", category: "advanced"}
sequenceGroupInterval: {description: "Bed files describing the regions to operate on.", category: "advanced"}
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.",
......@@ -59,7 +59,7 @@ task ApplyBQSR {
referenceFastaFai: {description: "The index for the reference fasta file.", 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.",
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"}
......@@ -108,6 +108,28 @@ task BaseRecalibrator {
docker: dockerImage
memory: memory
}
parameter_meta {
inputBam: {description: "The BAM file to generate a BQSR report for.", category: "required"}
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: "advancded"}
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"}
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"}
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 CombineGVCFs {
......
picard.wdl
+ 6
− 6
View file @ 0b2a14fc
......@@ -36,7 +36,7 @@ task BedToIntervalList {
outputPath: {description: "The location the output interval list 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.",
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"}
......@@ -164,7 +164,7 @@ task CollectMultipleMetrics {
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.",
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"}
......@@ -217,7 +217,7 @@ task CollectRnaSeqMetrics {
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.",
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"}
......@@ -282,7 +282,7 @@ task CollectTargetedPcrMetrics {
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.",
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"}
......@@ -329,7 +329,7 @@ task GatherBamFiles {
outputBamPath: {description: "The path where the merged BAM file will be written.", caregory: "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.",
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"}
......@@ -371,7 +371,7 @@ task GatherVcfs {
outputVcfPath: {description: "The path where the merged VCF file will be written.", caregory: "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.",
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"}
......
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