Update gatk with outputs.

eeff6ce5 · JasperBoom · 091c3e31 · eeff6ce5 · eeff6ce5
Commit eeff6ce5 authored 4 years ago by JasperBoom
--- 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."}
    }
 }
--- 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 {