add hmftools.wdl

hmftools.wdl

+version 1.0
+
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task Amber {
+    input {
+        String normalName
+        File normalBam
+        File normalBamIndex
+        String tumorName
+        File tumorBam
+        File tumorBamIndex
+        String outputDir = "./amber"
+        File loci
+        File referenceFasta
+        File referenceFastaFai
+        File referenceFastaDict
+
+        Int threads = 2
+        String memory = = "33G"
+        String javaXmx = "32G"
+        Int timeMinutes = 60
+        String dockerImage = "quay.io/biocontainers/hmftools-amber:3.5--0"
+    }
+
+    command {
+        AMBER -Xmx~{javaXmx} \
+        -reference ~{normalName} \
+        -reference_bam ~{normalBam} \
+        -tumor ~{tumorName} \
+        -tumor_bam ~{tumorBam} \
+        -output_dir ~{outputDir} \
+        -threads ~{threads} \
+        -ref_genome ~{referenceFasta} \
+        -loci ~{loci}
+    }
+
+    output {
+        File version = "amber.version"
+        File tumorBafPcf = "~{outputDir}/~{tumorName}.amber.baf.pcf"
+        File tumorBafTsv = "~{outputDir}/~{tumorName}.amber.baf.tsv"
+        File tumorBafVcf = "~{outputDir}/~{tumorName}.amber.baf.vcf.gz"
+        File tumorBafVcfIndex = "~{outputDir}/~{tumorName}.amber.baf.vcf.gz.tbi"
+        File tumorContaminationVcf = "~{outputDir}/~{tumorName}.amber.contamination.vcf.gz"
+        File tumorContaminationVcfIndex = "~{outputDir}/~{tumorName}.amber.contamination.vcf.gz.tbi"
+        File tumorContaminationTsv = "~{outputDir}/~{tumorName}.amber.contamination.tsv"
+        File tumorQc = "~{outputDir}/~{tumorName}.amber.qc"
+        File normalSnpVcf = "~{outputDir}/~{normalName}.amber.snp.vcf.gz"
+        File normalSnpVcfIndex = "~{outputDir}/~{normalName}.amber.snp.vcf.gz.tbi"
+        Array[File] outputs = [version, tumorBafPcf, tumorBafTsv, tumorBafVcf, tumorBafVcfIndex, 
+            tumorContaminationVcf, tumorContaminationVcfIndex, tumorContaminationTsv, tumorQc, 
+            normalSnpVcf, normalSnpVcfIndex]
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+        cpu: threads
+    }
+
+    parameter_meta {
+        normalName: {description: "the name of the normal sample.", category: "required"}
+        normalBam: {description: "The normal BAM file.", category: "required"}
+        normalBamIndex: {description: "The index for the normal BAM file.", category: "required"}
+        tumorName: {description: "The name of the tumor sample.", category: "required"}
+        tumorBam: {description: "The tumor BAM file.", category: "required"}
+        tumorBamIndex: {description: "The index for the tumor BAM file.", category: "required"}
+        outputDir: {description: "The path to the output directory.", category: "common"}
+        loci: {description: "A VCF file containing likely heterozygous sites.", category: "required"}
+        referenceFasta: {description: "The reference fasta file.", 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"}
+        threads: {description: "The number of threads the program will use.", 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"}
+        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"}
+    }
+}
+
+task Cobalt {
+    input {
+        String normalName
+        File normalBam
+        File normalBamIndex
+        String tumorName
+        File tumorBam
+        File tumorBamIndex
+        String outputDir = "./cobalt"
+        File gcProfile
+        
+        Int threads = 1
+        String memory = = "9G"
+        String javaXmx = "8G"
+        Int timeMinutes = 60
+        String dockerImage = "quay.io/biocontainers/hmftools-cobalt:1.10--0"
+    }
+
+    command {
+        COBALT -Xmx~{javaXmx} \
+        -reference ~{normalName} \
+        -reference_bam ~{normalBam} \
+        -tumor ~{tumorName} \
+        -tumor_bam ~{tumorBam} \
+        -output_dir ~{outputDir}\
+        -threads ~{threads} \
+        -gc_profile ~{gcProfile}
+    }
+
+    output {
+        File version = "cobalt.version"
+        File normalGcMedianTsv = "~{outputDir}/~{normalName}.cobalt.gc.median.tsv"
+        File normalRationMedianTsv = "~{outputDir}/~{normalName}.cobalt.ratio.median.tsv"
+        File normalRationPcf = "~{outputDir}/~{normalName}.cobalt.ratio.pcf"
+        File tumorGcMedianTsv = "~{outputDir}/~{tumorName}.cobalt.gc.median.tsv"
+        File tumorRatioPcf = "~{outputDir}/~{tumorName}.cobalt.ratio.pcf"
+        File tumorRatioTsv = "~{outputDir}/~{tumorName}.cobalt.ratio.tsv"
+        File tumorChrLen = "~{outputDir}/~{tumorName}.chr.len"
+        Array[File] outputs = [version, normalGcMedianTsv, normalRationMedianTsv,
+            normalRationPcf, tumorGcMedianTsv, tumorRatioPcf, tumorRatioTsv, tumorChrLen]
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+        cpu: threads
+    }
+
+    parameter_meta {
+        normalName: {description: "the name of the normal sample.", category: "required"}
+        normalBam: {description: "The normal BAM file.", category: "required"}
+        normalBamIndex: {description: "The index for the normal BAM file.", category: "required"}
+        tumorName: {description: "The name of the tumor sample.", category: "required"}
+        tumorBam: {description: "The tumor BAM file.", category: "required"}
+        tumorBamIndex: {description: "The index for the tumor BAM file.", category: "required"}
+        outputDir: {description: "The path to the output directory.", category: "common"}
+        gcProfile: {description: "A file describing the GC profile of the reference genome.", category: "required"}
+        threads: {description: "The number of threads the program will use.", 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"}
+        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"}
+    }
+}
+
+task GripssApplicationKt {
+    input {
+        File inputVcf
+        String outputPath = "gripss.vcf.gz"
+        File referenceFasta
+        File referenceFastaFai
+        File referenceFastaDict
+        File breakpointHotspot
+        File breakendPon
+        File breakpointPon
+
+        String memory = "25G"
+        String javaXmx = "24G"
+        Int timeMinutes = 60
+        String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.8--0"
+    }
+
+    command {
+        java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        -cp /usr/local/share/hmftools-gripss-1.8-0/gripss.jar \
+        com.hartwig.hmftools.gripss.GripssApplicationKt \
+        -ref_genome ~{referenceFasta} \
+        -breakpoint_hotspot ~{breakpointHotspot} \
+        -breakend_pon ~{breakendPon} \
+        -breakpoint_pon ~{breakpointPon} \
+        -input_vcf ~{inputVcf} \
+        -output_vcf ~{outputPath} 
+    }
+
+    output {
+        File outputVcf = outputPath
+        File outputVcfIndex = outputPath + ".tbi"
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        inputVcf: {description: "The input VCF.", category: "required"}
+        outputPath: {description: "The path where th eoutput VCF will be written.", category: "common"}
+        referenceFasta: {description: "The reference fasta file.", 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"}
+        breakpointHotspot: {description: "Equivalent to the `-breakpoint_hotspot` option.", category: "required"}
+        breakendPon: {description: "Equivalent to the `-breakend_pon` option.", category: "required"}
+        breakpointPon: {description: "Equivalent to the `breakpoint_pon` option.", 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"}
+        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"}
+    }
+}
+
+task GripssHardFilterApplicationKt {
+    input {
+        File inputVcf
+        String outputPath = "gripss_hard_filter.vcf.gz"
+
+        String memory = "25G"
+        String javaXmx = "24G"
+        Int timeMinutes = 60
+        String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.8--0"
+    }
+
+    command {
+        java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        -cp /usr/local/share/hmftools-gripss-1.8-0/gripss.jar \
+        com.hartwig.hmftools.gripss.GripssHardFilterApplicationKt \
+        -input_vcf ~{inputVcf} \
+        -output_vcf ~{outputPath} 
+    }
+
+    output {
+        File outputVcf = outputPath
+        File outputVcfIndex = outputPath + ".tbi"
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        inputVcf: {description: "The input VCF.", category: "required"}
+        outputPath: {description: "The path where th eoutput VCF will be written.", 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"}
+        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"}
+    }
+}
+
+task Purple {
+    input {
+        String normalName
+        String tumorName
+        String outputDir = "./purple"
+        Array[File]+ amberOutput
+        Array[File]+ cobaltOutput
+        File gcProfile
+        File somaticVcf
+        File filteredSvVcf
+        File fullSvVcf
+        File referenceFasta
+        File referenceFastaFai
+        File referenceFastaDict
+        File hotspots
+        
+        Int threads = 1
+        Int time_minutes = 60
+        String memory = "13G"
+        String javaXmx = "12G"
+        String docker = "quay.io/biocontainers/hmftools-purple:2.51--1"
+    }
+
+    command {
+        PURPLE -Xmx~{javaXmx} \
+        -reference ~{normalName} \
+        -tumor ~{tumorName} \
+        -output_dir ~{outputDir} \
+        -amber ~{sub(amberOutput, basename(amberOutput[0]), "")} \
+        -cobalt ~{sub(cobaltOutput, basename(cobaltOutput[0]), "")} \
+        -gc_profile ~{gcProfile} \
+        -somatic_vcf ~{somaticVcf} \
+        -structural_vcf ~{filteredSvVcf} \
+        -sv_recovery_vcf ~{fullSvVcf} \
+        -circos /usr/local/bin/circos \
+        -ref_genome ~{referenceFasta} \
+        -driver_catalog \
+        -hotspots ~{hotspots} \
+        -threads ~{threads}
+
+        # TODO if shallow also the following:
+        #-highly_diploid_percentage 0.88 \
+        #-somatic_min_total 100 \
+        #-somatic_min_purity_spread 0.1
+    }
+
+    output {
+        #TODO
+    }
+
+    runtime {
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        cpu: threads
+        docker: dockerImage
+        memory: memory
+    }
+
+    parameter_meta {
+        normalName: {description: "the name of the normal sample.", category: "required"}
+        tumorName: {description: "The name of the tumor sample.", category: "required"}
+        outputDir: {description: "The path to the output directory.", category: "common"}
+        amberOutput: {description: "The output files of hmftools amber.", category: "required"}
+        cobaltOutput: {description: "The output files of hmftools cobalt", category: "required"}
+        gcProfile: {description: "A file describing the GC profile of the reference genome.", category: "required"}
+        somaticVcf: {description: "The somatic variant calling results.", category: "required"}
+        filteredSvVcf: {description: "The filtered structural variant calling results.", category: "required"}
+        fullSvVcf: {description: "The unfiltered structural variant calling results.", category: "required"}
+        referenceFasta: {description: "The reference fasta file.", 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"}
+        hotspots: {description: "A vcf file with hotspot variant sites.", category: "required"}
+
+        threads: {description: "The number of threads the program will use.", 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"}
+        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"}
+    }
+}
+
+task Sage {
+    input {
+        String tumorName
+        File tumorBam
+        File tumorBamIndex
+        File referenceFasta
+        File referenceFastaDict
+        File referenceFastaFai
+        File hotspots
+        File panelBed
+        File highConfidenceBed
+        Boolean hg38 = false
+        String outputPath = "./sage.vcf.gz"
+
+        String? normalName
+        File? normalBam
+        File? normalBamIndex
+
+        Int threads = 2
+        String javaXmx = "32G"
+        String memory = "33G"
+        Int timeMinutes = 1 + ceil(size(select_all([tumorBam, normalBam]), "G") * 10 / threads) #FIXME make sure this is enough
+        String dockerImage = "quay.io/biocontainers/hmftools-sage:2.2--2"
+    }
+
+    command {
+        java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        -cp /usr/local/share/hmftools-sage-2.2-2/sage.jar \
+        com.hartwig.hmftools.sage.SageApplication \
+        -tumor ~{tumorName} \
+        -tumor_bam ~{tumorBam} \
+        ~{"-reference " + normalName} \
+        ~{"-reference_bam " + normalBam} \
+        -ref_genome ~{referenceFasta} \
+        -hotspots ~{hotspots} \
+        -panel_bed ~{panelBed} \
+        -high_confidence_bed ~{highConfidenceBed} \
+        -assembly ~{true="hg38" false="hg19" hg38} \
+        -threads ~{threads} \
+        -out ~{outputPath}
+    }
+
+    output {
+        File outputVcf = outputPath
+        File outputVcfIndex = outputPath + ".tbi"
+        # There is some plots as well, but in the current container the labels in the plots are just series of `□`s.
+        # This seems to be a systemic issue with R generated plots in biocontainers...
+    }
+
+    runtime {
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        cpu: threads
+        docker: dockerImage
+        memory: memory
+    }
+
+    parameter_meta {
+        tumorName: {description: "The name of the tumor sample.", category: "required"}
+        tumorBam: {description: "The BAM file for the tumor sample.", category: "required"}
+        tumorBamIndex: {description: "The index of the BAM file for the tumor sample.", category: "required"}
+        normalName: {description: "The name of the normal/reference sample.", category: "common"}
+        normalBam: {description: "The BAM file for the normal sample.", category: "common"}
+        normalBamIndex: {description: "The index of the BAM file for the normal sample.", category: "common"}
+        referenceFasta: {description: "The reference fasta file.", 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"}
+        hotspots: {description: "A vcf file with hotspot variant sites.", category: "required"}
+        panelBed: {description: "A bed file describing coding regions to search for in frame indels.", category: "required"}
+        highConfidenceBed: {description: "A bed files describing high confidence mapping regions.", 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"}
+        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"}
+    }
+}