From eeff6ce5e37f75aa508fec3bf9ba38bede23dd17 Mon Sep 17 00:00:00 2001
From: JasperBoom <jboom@infernum.nl>
Date: Mon, 9 Nov 2020 11:01:08 +0100
Subject: [PATCH] Update gatk with outputs.
---
gatk.wdl | 80 +++++++++++++++++++++++++++++++++++++++++++++++---
gffcompare.wdl | 9 ++++++
2 files changed, 85 insertions(+), 4 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index d13c117..82244ca 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -581,7 +581,8 @@ task CreateReadCountPanelOfNormals {
String javaXmx = "7G"
String memory = "8G"
Int timeMinutes = 5
- String dockerImage = "broadinstitute/gatk:4.1.8.0" # The biocontainer causes a spark related error for some reason...
+ # The biocontainer causes a spark related error for some reason.
+ String dockerImage = "broadinstitute/gatk:4.1.8.0"
}
command {
@@ -742,9 +743,9 @@ task FilterMutectCalls {
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"}
# outputs
- filteredVcf: {description: ""}
- filteredVcfIndex: {description: ""}
- filteringStats: {description: ""}
+ filteredVcf: {description: "VCF file with filtered variants from a Mutect2 VCF callset."}
+ filteredVcfIndex: {description: "Index of output VCF file."}
+ filteringStats: {description: "The output filtering stats file."}
}
}
@@ -787,6 +788,9 @@ task GatherBqsrReports {
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ outputBQSRreport: {description: "Single file with scattered BQSR recalibration reports gathered into one."}
}
}
@@ -840,6 +844,9 @@ task GenomicsDBImport {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ genomicsDbTarArchive: {description: "Imported VCFs to GenomicsDB file."}
}
}
@@ -907,6 +914,10 @@ task GenotypeGVCFs {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ outputVCF: {description: "A final VCF in which all samples have been jointly genotyped. "}
+ outputVCFIndex: {description: "Index of final VCF file."}
}
}
@@ -959,6 +970,9 @@ task GetPileupSummaries {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ pileups: {description: "Pileup metrics for inferring contamination."}
}
}
@@ -1047,6 +1061,10 @@ task HaplotypeCaller {
memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ outputVCF: {description: "Raw, unfiltered SNP and indel calls."}
+ outputVCFIndex: {description: "Index of output VCF."}
}
}
@@ -1085,6 +1103,9 @@ task LearnReadOrientationModel {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ artifactPriorsTable: {description: "Maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter."}
}
}
@@ -1123,6 +1144,9 @@ task MergeStats {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ mergedStats: {description: "Merged stats from scattered Mutect2 runs."}
}
}
@@ -1190,6 +1214,19 @@ task ModelSegments {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ hetrozygousAllelicCounts: {description: "Allelic-counts file containing the counts at sites genotyped as heterozygous in the case sample."}
+ copyRatioSegments: {description: "It contains the segments from the .modelFinal.seg file converted to a format suitable for input to CallCopyRatioSegments."}
+ copyRatioCBS: {description: "The posterior medians of the log2 copy ratio."}
+ alleleFractionCBS: {description: "Minor-allele fraction."}
+ unsmoothedModeledSegments: {description: "The initial modeled-segments result before segmentation smoothing."}
+ unsmoothedCopyRatioParameters: {description: "The initial copy-ratio-model global-parameter result before segmentation smoothing"}
+ unsmoothedAlleleFractionParameters: {description: "The initial allele-fraction-model global-parameter result before segmentation smoothing."}
+ modeledSegments: {description: "The final modeled-segments result after segmentation smoothing."}
+ copyRatioParameters: {description: "The final copy-ratio-model global-parameter result after segmentation smoothing"}
+ alleleFractionParameters: {description: "The final allele-fraction-model global-parameter result after segmentation smoothing."}
+ normalHetrozygousAllelicCounts: {description: "Allelic-counts file containing the counts at sites genotyped as heterozygous in the matched-normal sample."}
}
}
@@ -1268,6 +1305,12 @@ task MuTect2 {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ vcfFile: {description: "Somatic SNVs and indels called via local assembly of haplotypes."}
+ vcfFileIndex: {description: "Index for Mutect2 VCF."}
+ f1r2File: {description: "Contains information that can then be passed to LearnReadOrientationModel, which generate an artifact prior table for each tumor sample for FilterMutectCalls to use."}
+ stats: {description: "Stats file."}
}
}
@@ -1327,6 +1370,14 @@ task PlotDenoisedCopyRatios {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ denoisedCopyRatiosPlot: {description: "Plot showing the entire range of standardized and denoised copy ratios."}
+ standardizedMedianAbsoluteDeviation: {description: "Standardized median absolute deviation copy ratios."}
+ denoisedMedianAbsoluteDeviation: {description: "Denoised median absolute deviation copy ratios."}
+ deltaMedianAbsoluteDeviation: {description: "The change between `standardizedMedianAbsoluteDeviation` & `denoisedMedianAbsoluteDeviation`."}
+ deltaScaledMedianAbsoluteDeviation: {description: "The change between `standardizedMedianAbsoluteDeviation` & `denoisedMedianAbsoluteDeviation` scaled by standardized MAD."}
+ denoisedCopyRatiosLimitedPlot: {description: "Plot showing the standardized and denoised copy ratios limited to ratios within [0, 4]."}
}
}
@@ -1384,6 +1435,9 @@ task PlotModeledSegments {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ modeledSegmentsPlot: {description: "This plot shows the input denoised copy ratios and/or alternate-allele fractions as points, as well as box plots for the available posteriors in each segment."}
}
}
@@ -1443,6 +1497,9 @@ task PreprocessIntervals {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ intervalList: {description: "Preprocessed Picard interval-list file."}
}
}
@@ -1501,6 +1558,10 @@ task SelectVariants {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ outputVcf: {description: "A new VCF file containing the selected subset of variants."}
+ outputVcfIndex: {description: "Index of the new output VCF file."}
}
}
@@ -1555,6 +1616,10 @@ task SplitNCigarReads {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ bam: {description: "BAM file with reads split at N CIGAR elements and CIGAR strings updated."}
+ bamIndex: {description: "Index of output BAM file."}
}
}
@@ -1639,6 +1704,9 @@ task VariantEval {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ table: {description: "Evaluation tables detailing the results of the eval modules which were applied."}
}
}
@@ -1696,5 +1764,9 @@ task VariantFiltration {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ filteredVcf: {description: "A filtered VCF in which passing variants are annotated as PASS and failing variants are annotated with the name(s) of the filter(s) they failed. "}
+ filteredVcfIndex: {description: "Index of filtered VCF."}
}
}
diff --git a/gffcompare.wdl b/gffcompare.wdl
index 8bd5309..f8f0ade 100644
--- a/gffcompare.wdl
+++ b/gffcompare.wdl
@@ -142,6 +142,15 @@ task GffCompare {
namePrefix: {description: "Equivalent to gffcompare's `-p` option.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"}
+
+ # outputs
+ annotated: {description: ""}
+ loci: {description: ""}
+ stats: {description: ""}
+ tracking: {description: ""}
+ allFiles: {description: ""}
+ redundant: {description: ""}
+ missedIntrons: {description: ""}
}
meta {
--
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