diff --git a/extractSigPredictHRD.wdl b/extractSigPredictHRD.wdl
index 1520b608..b43d8daf 100644
--- a/extractSigPredictHRD.wdl
+++ b/extractSigPredictHRD.wdl
@@ -22,7 +22,7 @@ version 1.0
 
 task ExtractSigPredictHRD {
     input {
-        String outputDir = "."
+        String outputDir = "./chord"
         String sampleName
         File snvIndelVcf
         File snvIndelVcfIndex
@@ -36,8 +36,11 @@ task ExtractSigPredictHRD {
     }
 
     command {
+        set -e
+        mkdir -p ~{outputDir}
+        cd ~{outputDir}
         extractSigPredictHRD.R \
-        ~{outputDir} \
+        . \
         ~{sampleName} \
         ~{snvIndelVcf} \
         ~{svVcf} \
diff --git a/fastp.wdl b/fastp.wdl
index 9849738b..7df0a8f3 100644
--- a/fastp.wdl
+++ b/fastp.wdl
@@ -42,7 +42,7 @@ task Fastp {
         
         Int threads = 4
         String memory = "50GiB"
-        Int timeMinutes = 1 + ceil(size([read1, read2], "G")  * 6.0 / threads)
+        Int timeMinutes = 1 + ceil(size([read1, read2], "G")  * 7.0 / select_first([effectiveSplit, threads]))
         String dockerImage = "quay.io/biocontainers/fastp:0.23.2--h5f740d0_3"
 
         Int? noneInt
diff --git a/gridss.wdl b/gridss.wdl
index 5aca3825..c9ba9bac 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -26,15 +26,12 @@ task AnnotateInsertedSequence {
     input {
         File inputVcf
         String outputPath = "gridss.annotated.vcf.gz"
-        File viralReference
-        File viralReferenceFai
-        File viralReferenceDict
-        File viralReferenceImg
+        BwaIndex viralReferenceBwaIndex
 
         Int threads = 8
         String javaXmx = "8G"
         String memory = "9GiB"
-        String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+        String dockerImage = "quay.io/biocontainers/gridss:2.13.2--h20b1175_1"
         Int timeMinutes = 120
     }
 
@@ -42,7 +39,7 @@ task AnnotateInsertedSequence {
         set -e
         _JAVA_OPTIONS="$_JAVA_OPTIONS -Xmx~{javaXmx}"
         AnnotateInsertedSequence \
-        REFERENCE_SEQUENCE=~{viralReference} \
+        REFERENCE_SEQUENCE=~{viralReferenceBwaIndex.fastaFile} \
         INPUT=~{inputVcf} \
         OUTPUT=~{outputPath} \
         ALIGNMENT=APPEND \
@@ -65,10 +62,7 @@ task AnnotateInsertedSequence {
     parameter_meta {
         inputVcf: {description: "The input VCF file.", category: "required"}
         outputPath: {description: "The path the output will be written to.", category: "common"}
-        viralReference: {description: "A fasta file with viral sequences.", category: "required"}
-        viralReferenceFai: {description: "The index for the viral reference fasta.", category: "required"}
-        viralReferenceDict: {description: "The dict file for the viral reference.", category: "required"}
-        viralReferenceImg: {description: "The BWA index image (generated with GATK BwaMemIndexImageCreator) of the viral reference.", category: "required"}
+        viralReferenceBwaIndex: {description: "The BWA index of the viral reference.", 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.",
@@ -269,7 +263,7 @@ task GRIDSS {
         Int nonJvmMemoryGb = 10
         Int threads = 12
         Int timeMinutes = ceil(7200 / threads) + 1800
-        String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+        String dockerImage = "quay.io/biocontainers/gridss:2.13.2--h20b1175_1"
     }
 
     command {
@@ -305,7 +299,7 @@ task GRIDSS {
 
     runtime {
         cpu: threads
-        memory: "~{jvmHeapSizeGb + nonJvmMemoryGb}GiB"
+        memory: "~{jvmHeapSizeGb + nonJvmMemoryGb}G"
         time_minutes: timeMinutes # !UnknownRuntimeKey
         docker: dockerImage
     }
@@ -345,14 +339,14 @@ task GridssAnnotateVcfRepeatmasker {
 
         String memory = "25GiB"
         Int threads = 8
-        String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+        String dockerImage = "quay.io/biocontainers/gridss:2.13.2--h20b1175_1"
         Int timeMinutes = 1440
     }
 
     command {
         gridss_annotate_vcf_repeatmasker \
         --output ~{outputPath} \
-        --jar /usr/local/share/gridss-2.12.2-0/gridss.jar \
+        --jar /usr/local/share/gridss-2.13.2-1/gridss.jar \
         -w . \
         -t ~{threads} \
         ~{gridssVcf}
@@ -382,6 +376,83 @@ task GridssAnnotateVcfRepeatmasker {
     }
 }
 
+task GridssSvPrep {
+    input {
+        Array[String]+ tumorLabel
+        Array[File]+ tumorBam
+        Array[File]+ tumorBai
+        Array[File]+ tumorFilteredBam
+        Array[File]+ tumorFilteredBai
+        BwaIndex reference
+        File blacklistBed
+        File gridssProperties
+
+        String? normalLabel
+        File? normalBam
+        File? normalBai
+        File? normalFilteredBam
+        File? normalFilteredBai
+        String outputPath = "gridss.vcf.gz"
+
+        Int jvmHeapSizeGb = 48
+        Int nonJvmMemoryGb = 10
+        Int threads = 10
+        Int timeMinutes = ceil(7200 / threads) + 1800
+        String dockerImage = "quay.io/biowdl/gridss@sha256:f70696fda4b6f2612b21539d49986cf31bee7542a9eb0269a9f718f99df3fb2a"
+    }
+
+    command {
+        gridss_sv-prep \
+        --steps all \
+        --output ~{outputPath} \
+        --workingdir . \
+        --reference ~{reference.fastaFile} \
+        --jar /usr/local/share/gridss-2.13.2-1/gridss.jar \
+        --blacklist ~{blacklistBed} \
+        --configuration ~{gridssProperties} \
+        --labels ~{normalLabel}~{true="," false="" defined(normalLabel)}~{sep="," tumorLabel} \
+        --bams ~{normalBam}~{true="," false="" defined(normalBam)}~{sep="," tumorBam} \
+        --filtered_bams ~{normalFilteredBam}~{true="," false="" defined(normalFilteredBam)}~{sep="," tumorFilteredBam} \
+        --jvmheap ~{jvmHeapSizeGb}G \
+        --threads ~{threads}
+    }
+
+    output {
+        File vcf = outputPath
+        File vcfIndex = outputPath + ".tbi"
+    }
+
+    runtime {
+        cpu: threads
+        memory: "~{jvmHeapSizeGb + nonJvmMemoryGb}GiB"
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        tumorBam: {description: "The input BAM file. This should be the tumor/case sample in case of a paired analysis.", category: "required"}
+        tumorBai: {description: "The index for tumorBam.", category: "required"}
+        tumorFilteredBam: {description: "The input BAM file preprocessed by hmftools' sv-prep.", category: "required"}
+        tumorFilteredBai: {description: "The index for tumorFilteredBam.", category: "required"}
+        tumorLabel: {description: "The name of the (tumor) sample.", category: "required"}
+        reference: {description: "A BWA index, this should also include the fasta index file (.fai).", category: "required"}
+        outputPath: {description: "The path for the output VCf file.", category: "common"}
+        normalBam: {description: "The BAM file for the normal/control sample.", category: "advanced"}
+        normalBai: {description: "The index for normalBam.", category: "advanced"}
+        normalFilteredBam: {description: "The BAM file for the normal control sample preprocessed by hmftools' sv-prep.", category: "required"}
+        normalFilteredBai: {description: "The index for normalFilteredBam.", category: "required"}
+        normalLabel: {description: "The name of the normal sample.", category: "advanced"}
+        blacklistBed: {description: "A bed file with blaclisted regins.", category: "advanced"}
+        gridssProperties: {description: "A properties file for gridss.", category: "advanced"}
+
+        threads: {description: "The number of the threads to use.", category: "advanced"}
+        jvmHeapSizeGb: {description: "The size of JVM heap for assembly and variant calling", category: "advanced"}
+        nonJvmMemoryGb: {description: "The amount of memory in Gb to be requested besides JVM memory.", 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 SomaticFilter {
     input {
         File vcfFile
@@ -444,13 +515,13 @@ task Virusbreakend {
         File referenceFasta
         File referenceFastaFai
         File referenceFastaDict
-        File referenceImg
         File virusbreakendDB
         String outputPath = "./virusbreakend.vcf"
 
-        String memory = "75GiB"
+        Int extraMemoryGB = 10
+        Int gridssMemoryGB = 60
         Int threads = 12
-        String dockerImage = "quay.io/biowdl/gridss:2.12.2"
+        String dockerImage = "quay.io/biocontainers/gridss:2.13.2--h20b1175_1"
         Int timeMinutes = 320
     }
 
@@ -463,8 +534,9 @@ task Virusbreakend {
         --workingdir . \
         --reference ~{referenceFasta} \
         --db virusbreakenddb \
-        --jar /usr/local/share/gridss-2.12.2-0/gridss.jar \
+        --jar /usr/local/share/gridss-2.13.2-1/gridss.jar \
         -t ~{threads} \
+        --gridssargs '--jvmheap ~{gridssMemoryGB}G' \
         ~{bam}
     }
 
@@ -475,7 +547,7 @@ task Virusbreakend {
 
     runtime {
         cpu: threads
-        memory: memory
+        memory: "~{gridssMemoryGB + extraMemoryGB}GiB"
         time_minutes: timeMinutes # !UnknownRuntimeKey
         docker: dockerImage
     }
@@ -484,10 +556,10 @@ task Virusbreakend {
         bam: {description: "A BAM file.", category: "required"}
         bamIndex: {description: "The index for the BAM file.", category: "required"}
         referenceFasta: {description: "The fasta of the reference genome.", category: "required"}
-        referenceImg: {description: "The BWA index image (generated with GATK BwaMemIndexImageCreator) of the reference.", category: "required"}
         virusbreakendDB: {description: "A .tar.gz containing the virusbreakend database.", category: "required"}
         outputPath: {description: "The path the output should be written to.", category: "common"}
-        memory: {description: "The amount of memory this job will use.", category: "advanced"}
+        extraMemoryGB: {description: "Extra memory needed for the job in GB.", category: "advanced"}
+        gridssMemoryGB: {description: "Memory assigned to GRIDSS in GB.", category: "advanced"}
         threads: {description: "The number of the threads to 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.",
diff --git a/hmftools.wdl b/hmftools.wdl
index c27630a1..46422f15 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -22,9 +22,9 @@ version 1.0
 
 task Amber {
     input {
-        String referenceName
-        File referenceBam
-        File referenceBamIndex
+        String? referenceName
+        File? referenceBam
+        File? referenceBamIndex
         String tumorName
         File tumorBam
         File tumorBamIndex
@@ -33,40 +33,44 @@ task Amber {
         File referenceFasta
         File referenceFastaFai
         File referenceFastaDict
+        String refGenomeVersion
+
+        Int? tumorOnlyMinDepth
 
         Int threads = 2
         String memory = "85GiB"
         String javaXmx = "80G"
         Int timeMinutes = 480
-        String dockerImage = "quay.io/biocontainers/hmftools-amber:3.5--0"
+        String dockerImage = "quay.io/biocontainers/hmftools-amber:3.9--hdfd78af_1"
     }
 
     command {
         AMBER -Xmx~{javaXmx} \
-        -reference ~{referenceName} \
-        -reference_bam ~{referenceBam} \
+        ~{"-reference " + referenceName} \
+        ~{"-reference_bam " + referenceBam} \
         -tumor ~{tumorName} \
         -tumor_bam ~{tumorBam} \
         -output_dir ~{outputDir} \
         -threads ~{threads} \
         -ref_genome ~{referenceFasta} \
-        -loci ~{loci}
+        -ref_genome_version ~{refGenomeVersion} \
+        -loci ~{loci} \
+        ~{"-tumor-only-min-depth " + tumorOnlyMinDepth}
     }
 
     output {
         File version = "~{outputDir}/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 tumorBafTsv = "~{outputDir}/~{tumorName}.amber.baf.tsv.gz"
         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 normalHomozygousregionsTsv = "~{outputDir}/~{referenceName}.amber.homozygousregion.tsv"
         File normalSnpVcf = "~{outputDir}/~{referenceName}.amber.snp.vcf.gz"
         File normalSnpVcfIndex = "~{outputDir}/~{referenceName}.amber.snp.vcf.gz.tbi"
-        Array[File] outputs = [version, tumorBafPcf, tumorBafTsv, tumorBafVcf, tumorBafVcfIndex,
-            tumorContaminationVcf, tumorContaminationVcfIndex, tumorContaminationTsv, tumorQc,
+        Array[File] outputs = [version, tumorBafPcf, tumorBafTsv, tumorContaminationVcf,
+            tumorContaminationVcfIndex, tumorContaminationTsv, tumorQc, normalHomozygousregionsTsv,
             normalSnpVcf, normalSnpVcfIndex]
     }
 
@@ -90,6 +94,7 @@ task Amber {
         referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.",
                              category: "required"}
         referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
+        refGenomeVersion: {description: "The version of the reference genome: 37 or 38.", 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.",
@@ -102,31 +107,40 @@ task Amber {
 
 task Cobalt {
     input {
-        String referenceName
-        File referenceBam
-        File referenceBamIndex
+        String? referenceName
+        File? referenceBam
+        File? referenceBamIndex
         String tumorName
         File tumorBam
         File tumorBamIndex
         String outputDir = "./cobalt"
         File gcProfile
+        File refGenomeFile
+
+        File? tumorOnlyDiploidBed
+        File? targetRegionsNormalisationTsv
+        Int? pcfGamma
 
         Int threads = 1
         String memory = "5GiB"
         String javaXmx = "4G"
-        Int timeMinutes = 480
-        String dockerImage = "quay.io/biocontainers/hmftools-cobalt:1.11--0"
+        Int timeMinutes = 960
+        String dockerImage = "quay.io/biocontainers/hmftools-cobalt:1.13--hdfd78af_1"
     }
 
     command {
         COBALT -Xmx~{javaXmx} \
-        -reference ~{referenceName} \
-        -reference_bam ~{referenceBam} \
+        ~{"-reference " + referenceName} \
+        ~{"-reference_bam " + referenceBam} \
         -tumor ~{tumorName} \
         -tumor_bam ~{tumorBam} \
         -output_dir ~{outputDir} \
         -threads ~{threads} \
-        -gc_profile ~{gcProfile}
+        -gc_profile ~{gcProfile} \
+        -ref_genome ~{refGenomeFile} \
+        ~{"-tumor_only_diploid_bed " + tumorOnlyDiploidBed} \
+        ~{"-target_region " + targetRegionsNormalisationTsv} \
+        ~{"-pcf_gamma" + pcfGamma}
     }
 
     output {
@@ -136,10 +150,9 @@ task Cobalt {
         File normalRationPcf = "~{outputDir}/~{referenceName}.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"
+        File tumorRatioTsv = "~{outputDir}/~{tumorName}.cobalt.ratio.tsv.gz"
         Array[File] outputs = [version, normalGcMedianTsv, normalRationMedianTsv,
-            normalRationPcf, tumorGcMedianTsv, tumorRatioPcf, tumorRatioTsv, tumorChrLen]
+            normalRationPcf, tumorGcMedianTsv, tumorRatioPcf, tumorRatioTsv]
     }
 
     runtime {
@@ -158,6 +171,7 @@ task Cobalt {
         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"}
+        refGenomeFile: {description: "The reference genome 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.",
@@ -176,7 +190,7 @@ task CupGenerateReport {
 
         String memory = "5GiB"
         Int timeMinutes = 10
-        String dockerImage = "quay.io/biowdl/cuppa:1.6"
+        String dockerImage = "quay.io/biowdl/cuppa@sha256:e76d367a3226068967fb64ad6adaa889cbdcc01397075b0cbc382bbba4350b98"
     }
 
     # This script writes to the directory that the input is located in.
@@ -232,34 +246,29 @@ task Cuppa {
     input {
         Array[File]+ linxOutput
         Array[File]+ purpleOutput
+        File virusInterpreterOutput
         String sampleName
         Array[String]+ categories = ["DNA"]
         Array[File]+ referenceData
-        File purpleSvVcf
-        File purpleSvVcfIndex
-        File purpleSomaticVcf
-        File purpleSomaticVcfIndex
         String outputDir = "./cuppa"
 
         String javaXmx = "4G"
         String memory = "5GiB"
         Int timeMinutes = 10
-        String dockerImage = "quay.io/biowdl/cuppa:1.6"
+        String dockerImage = "quay.io/biowdl/cuppa@sha256:e76d367a3226068967fb64ad6adaa889cbdcc01397075b0cbc382bbba4350b98"
     }
 
     command {
         set -e
         mkdir -p sampleData ~{outputDir}
         ln -s -t sampleData ~{sep=" " linxOutput} ~{sep=" " purpleOutput}
+        ln -s -t sampleData ~{virusInterpreterOutput}
         cuppa -Xmx~{javaXmx} \
         -output_dir ~{outputDir} \
-        -output_id ~{sampleName} \
         -categories '~{sep="," categories}' \
         -ref_data_dir ~{sub(referenceData[0], basename(referenceData[0]), "")} \
         -sample_data_dir sampleData \
-        -sample_data ~{sampleName} \
-        -sample_sv_file ~{purpleSvVcf} \
-        -sample_somatic_vcf ~{purpleSomaticVcf}
+        -sample_data ~{sampleName}
     }
 
     output {
@@ -278,10 +287,6 @@ task Cuppa {
         sampleName: {description: "The name of the sample.", category: "required"}
         categories: {description: "The classifiers to use.", category: "advanced"}
         referenceData : {description: "The reference data.", category: "required"}
-        purpleSvVcf: {description: "The VCF file produced by purple which contains structural variants.", category: "required"}
-        purpleSvVcfIndex: {description: "The index of the structural variants VCF file produced by purple.", category: "required"}
-        purpleSomaticVcf: {description: "The VCF file produced by purple which contains somatic variants.", category: "required"}
-        purpleSomaticVcfIndex: {description: "The index of the somatic VCF file produced by purple.", category: "required"}
         outputDir: {description: "The directory the ouput will be placed in.", 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.",
@@ -300,7 +305,7 @@ task CuppaChart {
 
         String memory = "4GiB"
         Int timeMinutes = 5
-        String dockerImage = "quay.io/biowdl/cuppa:1.6"
+        String dockerImage = "quay.io/biowdl/cuppa@sha256:e76d367a3226068967fb64ad6adaa889cbdcc01397075b0cbc382bbba4350b98"
     }
 
     command {
@@ -342,16 +347,24 @@ task Gripss {
         File knownFusionPairBedpe
         File breakendPon
         File breakpointPon
-        String referenceName
-        String tumorName
+        File repeatMaskFile
+        String? referenceName
+        String sampleName
         File vcf
         File vcfIndex
+        String outputId
         String outputDir = "./"
+        Boolean hg38 = false
+        Int? hardMinTumorQual
+        Int? minQualBreakPoint
+        Int? minQualBreakEnd
+        Boolean filterSgls = false
+        Boolean germline = false
 
         String memory = "17GiB"
         String javaXmx = "16G"
         Int timeMinutes = 50
-        String dockerImage = "quay.io/biocontainers/hmftools-gripss:2.0--hdfd78af_0"
+        String dockerImage = "quay.io/biocontainers/hmftools-gripss:2.3.2--hdfd78af_0"
     }
 
     command {
@@ -359,21 +372,30 @@ task Gripss {
         mkdir -p ~{outputDir}
         gripss -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
         -ref_genome ~{referenceFasta} \
+        -ref_genome_version ~{if hg38 then "38" else "37"} \
         -known_hotspot_file ~{knownFusionPairBedpe} \
         -pon_sgl_file ~{breakendPon} \
         -pon_sv_file ~{breakpointPon} \
-        -reference ~{referenceName} \
-        -sample ~{tumorName} \
+        -repeat_mask_file ~{repeatMaskFile} \
+        ~{"-reference " + referenceName} \
+        -sample ~{sampleName} \
         -vcf ~{vcf} \
         -output_dir ~{outputDir} \
-        -output_id somatic
+        -output_id ~{outputId} \
+        ~{if filterSgls then "-filter_sgls" else ""} \
+        ~{"-hard_min_tumor_qual " + hardMinTumorQual} \
+        ~{"-min_qual_break_point " + minQualBreakPoint} \
+        ~{"-min_qual_break_end " + minQualBreakEnd} \
+        ~{if germline then "-germline" else ""}
     }
 
+    String suffix = if defined(referenceName) then "somatic" else "germline"
+
     output {
-        File fullVcf = "~{outputDir}/~{tumorName}.gripss.somatic.vcf.gz"
-        File fullVcfIndex = "~{outputDir}/~{tumorName}.gripss.somatic.vcf.gz.tbi"
-        File filteredVcf = "~{outputDir}/~{tumorName}.gripss.filtered.somatic.vcf.gz"
-        File filteredVcfIndex = "~{outputDir}/~{tumorName}.gripss.filtered.somatic.vcf.gz.tbi"
+        File fullVcf = "~{outputDir}/~{sampleName}.gripss.~{suffix}.vcf.gz"
+        File fullVcfIndex = "~{outputDir}/~{sampleName}.gripss.~{suffix}.vcf.gz.tbi"
+        File filteredVcf = "~{outputDir}/~{sampleName}.gripss.filtered.~{suffix}.vcf.gz"
+        File filteredVcfIndex = "~{outputDir}/~{sampleName}.gripss.filtered.~{suffix}.vcf.gz.tbi"
     }
 
     runtime {
@@ -390,7 +412,7 @@ task Gripss {
         knownFusionPairBedpe: {description: "Equivalent to the `-known_hotspot_file` option.", category: "required"}
         breakendPon: {description: "Equivalent to the `-pon_sgl_file` option.", category: "required"}
         breakpointPon: {description: "Equivalent to the `-pon_sv_file` option.", category: "required"}
-        tumorName: {description: "The name of the tumor sample.", category: "required"}
+        sampleName: {description: "The name of the tumor sample.", category: "required"}
         referenceName: {description: "The name of the normal sample.", category: "required"}
         vcf: {description: "The input VCF.", category: "required"}
         vcfIndex: {description: "The index for the input VCF.", category: "required"}
@@ -405,116 +427,6 @@ task Gripss {
     }
 }
 
-task GripssApplicationKt {
-    # Obsolete
-    input {
-        File inputVcf
-        String outputPath = "gripss.vcf.gz"
-        String tumorName
-        String referenceName
-        File referenceFasta
-        File referenceFastaFai
-        File referenceFastaDict
-        File breakpointHotspot
-        File breakendPon
-        File breakpointPon
-
-        String memory = "32GiB"
-        String javaXmx = "31G"
-        Int timeMinutes = 45
-        String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.11--hdfd78af_0"
-    }
-
-    command {
-        java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-        -cp /usr/local/share/hmftools-gripss-1.11-0/gripss.jar \
-        com.hartwig.hmftools.gripss.GripssApplicationKt \
-        -tumor ~{tumorName} \
-        -reference ~{referenceName} \
-        -ref_genome ~{referenceFasta} \
-        -breakpoint_hotspot ~{breakpointHotspot} \
-        -breakend_pon ~{breakendPon} \
-        -breakpoint_pon ~{breakpointPon} \
-        -input_vcf ~{inputVcf} \
-        -output_vcf ~{outputPath} \
-        -paired_normal_tumor_ordinals
-    }
-
-    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"}
-        referenceName: {description: "The name of the normal sample.", category: "required"}
-        tumorName: {description: "The name of the tumor sample.", 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"}
-        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 {
-    # Obsolete
-    input {
-        File inputVcf
-        String outputPath = "gripss_hard_filter.vcf.gz"
-
-        String memory = "3GiB"
-        String javaXmx = "2G"
-        Int timeMinutes = 15
-        String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.11--hdfd78af_0"
-    }
-
-    command {
-        java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-        -cp /usr/local/share/hmftools-gripss-1.11-0/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 HealthChecker {
     input {
         String outputDir = "."
@@ -529,7 +441,7 @@ task HealthChecker {
         String javaXmx = "2G"
         String memory = "3GiB"
         Int timeMinutes = 1
-        String dockerImage = "quay.io/biowdl/health-checker:3.2"
+        String dockerImage = "quay.io/biowdl/health-checker:3.4"
     }
 
     command {
@@ -585,19 +497,84 @@ task HealthChecker {
     }
 }
 
+task Lilac {
+    input {
+        String sampleName
+        File referenceBam
+        File referenceBamIndex
+        File? tumorBam
+        File? tumorBamIndex
+        String refGenomeVersion
+        File referenceFasta
+        File referenceFastaFai
+        File referenceFastaDict
+        File? geneCopyNumberFile
+        File? somaticVariantsFile
+        File? somaticVariantsFileIndex
+        String outputDir = "./lilac"
+
+        #The following need to be in the same directory
+        File hlaRefAminoacidSequencesCsv
+        File hlaRefNucleotideSequencesCsv
+        File lilacAlleleFrequenciesCsv
+
+        String javaXmx = "15G"
+        String memory = "16GiB"
+        Int timeMinutes = 1440 #FIXME
+        Int threads = 1
+        String dockerImage = "quay.io/biocontainers/hmftools-lilac:1.4.2--hdfd78af_0"
+    }
+
+    command {
+        LILAC -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        -sample ~{sampleName} \
+        -reference_bam ~{referenceBam} \
+        -ref_genome ~{referenceFasta} \
+        -ref_genome_version ~{refGenomeVersion} \
+        -resource_dir ~{sub(hlaRefAminoacidSequencesCsv, basename(hlaRefAminoacidSequencesCsv), "")} \
+        -output_dir ~{outputDir} \
+        -threads ~{threads} \
+        ~{"-tumor_bam " + tumorBam} \
+        ~{"-gene_copy_number " + geneCopyNumberFile} \
+        ~{"-somatic_vcf " + somaticVariantsFile}
+    }
+
+    output {
+        File lilacCsv = "~{outputDir}/~{sampleName}.lilac.csv"
+        File lilacQcCsv = "~{outputDir}/~{sampleName}.lilac.qc.csv"
+        File candidatesCoverageCsv = "~{outputDir}/~{sampleName}.candidates.coverage.csv"
+    }
+
+    runtime {
+        memory: memory
+        cpu: threads
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+    }
+
+    parameter_meta {
+
+    }
+}
+
+
 task Linx {
     input {
         String sampleName
         File svVcf
         File svVcfIndex
-        Array[File]+ purpleOutput
+        Array[File] purpleOutput = []
         String refGenomeVersion
         String outputDir = "./linx"
-        File fragileSiteCsv
+        File? fragileSiteCsv
         File lineElementCsv
-        File knownFusionCsv
+        File? knownFusionCsv
         File driverGenePanel
         Boolean writeAllVisFusions = false
+        Boolean germline = false
+        Boolean checkFusions = true
+        Boolean checkDrivers = true
+        Boolean writeVisData = true
         #The following should be in the same directory.
         File geneDataCsv
         File proteinFeaturesCsv
@@ -607,47 +584,56 @@ task Linx {
         String memory = "9GiB"
         String javaXmx = "8G"
         Int timeMinutes = 10
-        String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
+        String dockerImage = "quay.io/biocontainers/hmftools-linx:1.22.1--hdfd78af_0"
+
+        String? DONOTDEFINE
     }
 
+    String? purpleDir = if length(purpleOutput) > 0
+        then sub(purpleOutput[0], basename(purpleOutput[0]), "")
+        else DONOTDEFINE
+
     command {
         linx -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
         -sample ~{sampleName} \
         -sv_vcf ~{svVcf} \
-        -purple_dir ~{sub(purpleOutput[0], basename(purpleOutput[0]), "")} \
+        ~{"-purple_dir " + purpleDir} \
         -ref_genome_version ~{refGenomeVersion} \
         -output_dir ~{outputDir} \
-        -fragile_site_file ~{fragileSiteCsv} \
+        ~{"-fragile_site_file " + fragileSiteCsv} \
         -line_element_file ~{lineElementCsv} \
         -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
-        -check_fusions \
-        -known_fusion_file ~{knownFusionCsv} \
-        -check_drivers \
+        ~{if checkFusions then "-check_fusions" else ""} \
+        ~{"-known_fusion_file " + knownFusionCsv} \
+        ~{if checkDrivers then "-check_drivers" else ""} \
         -driver_gene_panel ~{driverGenePanel} \
-        -chaining_sv_limit 0 \
-        -write_vis_data \
-        ~{if writeAllVisFusions then "-write_all_vis_fusions" else ""}
+        ~{if writeVisData then "-write_vis_data" else ""} \
+        ~{if writeAllVisFusions then "-write_all_vis_fusions" else ""} \
+        ~{if germline then "-germline" else ""}
     }
 
+    String prefix = if germline then "~{sampleName}.linx.germline" else "~{sampleName}.linx"
+
     output {
-        File driverCatalog = "~{outputDir}/~{sampleName}.linx.driver.catalog.tsv"
-        File linxBreakend = "~{outputDir}/~{sampleName}.linx.breakend.tsv"
-        File linxClusters = "~{outputDir}/~{sampleName}.linx.clusters.tsv"
-        File linxDrivers = "~{outputDir}/~{sampleName}.linx.drivers.tsv"
-        File linxFusion = "~{outputDir}/~{sampleName}.linx.fusion.tsv"
-        File linxLinks = "~{outputDir}/~{sampleName}.linx.links.tsv"
-        File linxSvs = "~{outputDir}/~{sampleName}.linx.svs.tsv"
-        File linxVisCopyNumber = "~{outputDir}/~{sampleName}.linx.vis_copy_number.tsv"
-        File linxVisFusion = "~{outputDir}/~{sampleName}.linx.vis_fusion.tsv"
-        File linxVisGeneExon = "~{outputDir}/~{sampleName}.linx.vis_gene_exon.tsv"
-        File linxVisProteinDomain = "~{outputDir}/~{sampleName}.linx.vis_protein_domain.tsv"
-        File linxVisSegments = "~{outputDir}/~{sampleName}.linx.vis_segments.tsv"
-        File linxVisSvData = "~{outputDir}/~{sampleName}.linx.vis_sv_data.tsv"
+        File driverCatalog = "~{outputDir}/~{prefix}.driver.catalog.tsv"
+        File linxClusters = "~{outputDir}/~{prefix}.clusters.tsv"
+        File linxLinks = "~{outputDir}/~{prefix}.links.tsv"
+        File linxSvs = "~{outputDir}/~{prefix}.svs.tsv"
+        File? linxBreakend = "~{outputDir}/~{prefix}.breakend.tsv"
+        File? linxDrivers = "~{outputDir}/~{prefix}.drivers.tsv"
+        File? linxFusion = "~{outputDir}/~{prefix}.fusion.tsv"
+        File? linxVisCopyNumber = "~{outputDir}/~{prefix}.vis_copy_number.tsv"
+        File? linxVisFusion = "~{outputDir}/~{prefix}.vis_fusion.tsv"
+        File? linxVisGeneExon = "~{outputDir}/~{prefix}.vis_gene_exon.tsv"
+        File? linxVisProteinDomain = "~{outputDir}/~{prefix}.vis_protein_domain.tsv"
+        File? linxVisSegments = "~{outputDir}/~{prefix}.vis_segments.tsv"
+        File? linxVisSvData = "~{outputDir}/~{prefix}.vis_sv_data.tsv"
+        File? linxDisruptionTsv = "~{outputDir}/~{prefix}.disruption.tsv"
         File linxVersion = "~{outputDir}/linx.version"
-        Array[File] outputs = [driverCatalog, linxBreakend, linxClusters, linxDrivers, linxFusion,
+        Array[File] outputs = select_all([driverCatalog, linxBreakend, linxClusters, linxDrivers, linxFusion,
                                linxLinks, linxSvs, linxVisCopyNumber, linxVisFusion,
                                linxVisGeneExon, linxVisProteinDomain, linxVisSegments, linxVisSvData,
-                               linxVersion]
+                               linxDisruptionTsv, linxVersion])
     }
 
     runtime {
@@ -684,7 +670,7 @@ task Linx {
 
 task LinxVisualisations {
     input {
-        String outputDir = "./linx_visualisation"
+        String outputDir = "./linx"
         String sample
         String refGenomeVersion
         Array[File]+ linxOutput
@@ -693,14 +679,14 @@ task LinxVisualisations {
         String memory = "9GiB"
         String javaXmx = "8G"
         Int timeMinutes = 1440
-        String dockerImage = "quay.io/biocontainers/hmftools-linx:1.18--hdfd78af_0"
+        String dockerImage = "quay.io/biocontainers/hmftools-linx:1.22.1--hdfd78af_0"
     }
 
     command {
         set -e
         mkdir -p ~{outputDir}
         java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-        -cp /usr/local/share/hmftools-linx-1.18-0/sv-linx.jar \
+        -cp /usr/local/share/hmftools-linx-1.22.1-0/linx.jar \
         com.hartwig.hmftools.linx.visualiser.SvVisualiser \
         -sample ~{sample} \
         -ref_genome_version ~{refGenomeVersion} \
@@ -754,19 +740,25 @@ task Orange {
         File sageSomaticTumorSampleBqrPlot
         File purpleGeneCopyNumberTsv
         File purpleGermlineDriverCatalogTsv
+        File purpleGermlineDeletionTsv
         File purpleGermlineVariantVcf
         File purpleGermlineVariantVcfIndex
         Array[File]+ purplePlots
         File purplePurityTsv
         File purpleQcFile
+        File purpleSomaticCopyNumberFile
         File purpleSomaticDriverCatalogTsv
         File purpleSomaticVariantVcf
         File purpleSomaticVariantVcfIndex
+        File lilacQcCsv
+        File lilacResultCsv
         File linxFusionTsv
         File linxBreakendTsv
         File linxDriverCatalogTsv
         File linxDriverTsv
+        File linxGermlineDisruptionTsv
         Array[File]+ linxPlots
+        File linxStructuralVariantTsv
         File cuppaResultCsv
         File cuppaSummaryPlot
         File? cuppaFeaturePlot
@@ -777,18 +769,23 @@ task Orange {
         #File pipelineVersionFile
         File cohortMappingTsv
         File cohortPercentilesTsv
+        Boolean hg38 = false
+        File driverGenePanel
+        File knownFusionFile
 
         String memory = "17GiB"
         String javaXmx = "16G"
         Int timeMinutes = 10
-        String dockerImage = "quay.io/biowdl/orange:v1.6"
+        String dockerImage = "quay.io/biocontainers/hmftools-orange:1.10.2--hdfd78af_0"
     }
 
     command {
         set -e
         mkdir -p ~{outputDir}
+        export JAVA_TOOL_OPTIONS='--add-opens=java.base/java.time=ALL-UNNAMED'
         orange -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
         -output_dir ~{outputDir} \
+        -ref_genome_version ~{if hg38 then "38" else "37"} \
         -doid_json ~{doidJson} \
         -primary_tumor_doids '~{sep=";" sampleDoids}' \
         -max_evidence_level C \
@@ -803,17 +800,23 @@ task Orange {
         -sage_somatic_tumor_sample_bqr_plot ~{sageSomaticTumorSampleBqrPlot} \
         -purple_gene_copy_number_tsv ~{purpleGeneCopyNumberTsv} \
         -purple_germline_driver_catalog_tsv ~{purpleGermlineDriverCatalogTsv} \
+        -purple_germline_deletion_tsv ~{purpleGermlineDeletionTsv} \
         -purple_germline_variant_vcf ~{purpleGermlineVariantVcf} \
         -purple_plot_directory ~{sub(purplePlots[0], basename(purplePlots[0]), "")} \
         -purple_purity_tsv ~{purplePurityTsv} \
         -purple_qc_file ~{purpleQcFile} \
+        -purple_somatic_copy_number_tsv ~{purpleSomaticCopyNumberFile} \
         -purple_somatic_driver_catalog_tsv ~{purpleSomaticDriverCatalogTsv} \
         -purple_somatic_variant_vcf ~{purpleSomaticVariantVcf} \
+        -lilac_qc_csv ~{lilacQcCsv} \
+        -lilac_result_csv ~{lilacResultCsv} \
         -linx_fusion_tsv ~{linxFusionTsv} \
         -linx_breakend_tsv ~{linxBreakendTsv} \
         -linx_driver_catalog_tsv ~{linxDriverCatalogTsv} \
         -linx_driver_tsv ~{linxDriverTsv} \
+        -linx_germline_disruption_tsv ~{linxGermlineDisruptionTsv} \
         -linx_plot_directory ~{sub(linxPlots[0], basename(linxPlots[0]), "")} \
+        -linx_structural_variant_tsv ~{linxStructuralVariantTsv} \
         -cuppa_result_csv ~{cuppaResultCsv} \
         -cuppa_summary_plot ~{cuppaSummaryPlot} \
         ~{"-cuppa_feature_plot " + cuppaFeaturePlot} \
@@ -822,9 +825,10 @@ task Orange {
         -protect_evidence_tsv ~{protectEvidenceTsv} \
         -annotated_virus_tsv ~{annotatedVirusTsv} \
         -cohort_mapping_tsv ~{cohortMappingTsv} \
-        -cohort_percentiles_tsv ~{cohortPercentilesTsv}
+        -cohort_percentiles_tsv ~{cohortPercentilesTsv} \
+        -driver_gene_panel_tsv ~{driverGenePanel} \
+        -known_fusion_file ~{knownFusionFile}
     }
-    #TODO may need to be added: -pipeline_version_file ~{pipelineVersionFile}
 
     output {
         File orangeJson = "~{outputDir}/~{tumorName}.orange.json"
@@ -894,18 +898,37 @@ task Pave {
         File referenceFastaDict
         String refGenomeVersion
         File driverGenePanel
+        File mappabilityBed
+        Array[File] gnomadFreqFiles = []
+
         #The following should be in the same directory.
         File geneDataCsv
         File proteinFeaturesCsv
         File transExonDataCsv
         File transSpliceDataCsv
 
+        File? ponFile
+        File? ponArtefactFile
+        String? ponFilters
+        File? clinvarVcf
+        File? clinvarVcfIndex
+        File? blacklistVcf
+        File? blacklistBed
+        File? blacklistVcfIndex
+        Boolean writePassOnly = false
+
         Int timeMinutes = 50
         String javaXmx = "8G"
         String memory = "9GiB"
-        String dockerImage = "quay.io/biowdl/pave:v1.0"
+        String dockerImage = "quay.io/biocontainers/hmftools-pave:1.4.1--hdfd78af_0"
+
+        String? DONOTDEFINE
     }
 
+    String? gnomadFreqDir = if length(gnomadFreqFiles) > 0
+        then sub(gnomadFreqFiles[0], basename(gnomadFreqFiles[0]), "")
+        else DONOTDEFINE
+
     command {
         set -e
         mkdir -p ~{outputDir}
@@ -916,7 +939,18 @@ task Pave {
         -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
         -ref_genome ~{referenceFasta} \
         -ref_genome_version ~{refGenomeVersion} \
-        -driver_gene_panel ~{driverGenePanel}
+        -driver_gene_panel ~{driverGenePanel} \
+        -read_pass_only \
+        -mappability_bed ~{mappabilityBed} \
+        ~{"-pon_file " + ponFile} \
+        ~{"-pon_artefact_file " + ponArtefactFile} \
+        ~{if defined(ponFilters) then ("-pon_filters '" + ponFilters + "'") else ""} \
+        ~{"-gnomad_freq_dir " + gnomadFreqDir} \
+        ~{if defined(gnomadFreqDir) then "-gnomad_load_chr_on_demand" else ""} \
+        ~{"-clinvar_vcf " + clinvarVcf} \
+        ~{"-blacklist_bed " + blacklistBed} \
+        ~{"-blacklist_vcf " + blacklistVcf} \
+        ~{if writePassOnly then "-write_pass_only" else ""}
     }
 
     output {
@@ -945,7 +979,16 @@ task Pave {
         proteinFeaturesCsv: {description: "A  CSV file containing protein feature information, must be in the same directory as `geneDataCsv`, `transExonDataCsv` and `transSpliceDataCsv`.", category: "required"}
         transExonDataCsv: {description: "A  CSV file containing transcript exon information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transSpliceDataCsv`.", category: "required"}
         transSpliceDataCsv: {description: "A  CSV file containing transcript splicing information, must be in the same directory as `geneDataCsv`, `proteinFeaturesCsv` and `transExonDataCsv`.", category: "required"}
-
+        mappabilityBed: {description: "A bed file with mappability information.", category: "required"}
+        ponFile: {description: "A panel of normals files.", category: "common"}
+        ponArtefactFile: {description: "A panel of normals artefact file.", category: "common"}
+        ponFilters: {description: "Filters to be applied based on the panel of normals.", category: "common"}
+        gnomadFreqFiles: {description: "A directory with gnomad frequency information.", category: "common"}
+        clinvarVcf: {description: "A clinvar VCF file.", category: "common"}
+        clinvarVcfIndex: {description: "The index for the clinvar VCF file.", category: "common"}
+        blacklistVcf: {description: "A blacklist VCF file.", category: "common"}
+        blacklistBed: {description: "A blacklist bed file.", category: "common"}
+        blacklistVcfIndex: {description: "The index for the blacklist vcf file.", 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"}
@@ -961,7 +1004,7 @@ task Protect {
         String tumorName
         String referenceName
         Array[String]+ sampleDoids
-        String outputDir = "."
+        String outputDir = "./protect"
         Array[File]+ serveActionability
         File doidJson
         File purplePurity
@@ -978,21 +1021,25 @@ task Protect {
         File linxDriversCatalog
         File chordPrediction
         File annotatedVirus
+        File lilacResultCsv
+        File lilacQcCsv
+        File driverGeneTsv
 
         String memory = "9GiB"
         String javaXmx = "8G"
         Int timeMinutes = 60
-        String dockerImage = "quay.io/biowdl/protect:v2.0"
+        String dockerImage = "quay.io/biocontainers/hmftools-protect:2.3--hdfd78af_0"
     }
 
     command {
-        protect -Xmx~{javaXmx} \
+        protect -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
         -ref_genome_version ~{refGenomeVersion} \
         -tumor_sample_id ~{tumorName} \
         -reference_sample_id ~{referenceName} \
         -primary_tumor_doids '~{sep=";" sampleDoids}' \
         -output_dir ~{outputDir} \
         -serve_actionability_dir ~{sub(serveActionability[0], basename(serveActionability[0]), "")} \
+        -driver_gene_tsv ~{driverGeneTsv} \
         -doid_json ~{doidJson} \
         -purple_purity_tsv ~{purplePurity} \
         -purple_qc_file ~{purpleQc} \
@@ -1005,7 +1052,9 @@ task Protect {
         -linx_breakend_tsv ~{linxBreakend} \
         -linx_driver_catalog_tsv ~{linxDriversCatalog} \
         -chord_prediction_txt ~{chordPrediction} \
-        -annotated_virus_tsv ~{annotatedVirus}
+        -annotated_virus_tsv ~{annotatedVirus} \
+        -lilac_result_csv ~{lilacResultCsv} \
+        -lilac_qc_csv ~{lilacQcCsv}
     }
 
     output {
@@ -1052,14 +1101,14 @@ task Protect {
 
 task Purple {
     input {
-        String referenceName
+        String? referenceName
         String tumorName
         String outputDir = "./purple"
         Array[File]+ amberOutput
         Array[File]+ cobaltOutput
         File gcProfile
         File somaticVcf
-        File germlineVcf
+        File? germlineVcf
         File filteredSvVcf
         File filteredSvVcfIndex
         File fullSvVcf
@@ -1067,11 +1116,18 @@ task Purple {
         File referenceFasta
         File referenceFastaFai
         File referenceFastaDict
+        String refGenomeVersion
         File driverGenePanel
         File somaticHotspots
-        File germlineHotspots
+        File? germlineHotspots
+        File? germlineDelFreqFile
         Float? highlyDiploidPercentage
         Float? somaticMinPuritySpread
+        File? targetRegionsBed
+        File? targetRegionsRatios
+        File? targetRegionsMsiIndels
+        Int? minDiploidTumorRatioCount
+        Int? minDiploidTumorRatioCountCentromere
         #The following should be in the same directory.
         File geneDataCsv
         File proteinFeaturesCsv
@@ -1083,14 +1139,16 @@ task Purple {
         String memory = "9GiB"
         String javaXmx = "8G"
         # clone of quay.io/biocontainers/hmftools-purple:3.2--hdfd78af_0 with 'ln -s /usr/local/lib/libwebp.so.7 /usr/local/lib/libwebp.so.6'
-        String dockerImage = "quay.io/biowdl/hmftools-purple:3.2"
+        #String dockerImage = "quay.io/biowdl/hmftools-purple:3.2" FIXME see if biocontainer works
+        String dockerImage = "quay.io/biocontainers/hmftools-purple:3.7.1--hdfd78af_0"
     }
 
     command {
-        PURPLE -Xmx~{javaXmx} \
-        -reference ~{referenceName} \
-        -germline_vcf ~{germlineVcf} \
-        -germline_hotspots ~{germlineHotspots} \
+        PURPLE -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        ~{"-reference " + referenceName} \
+        ~{"-germline_vcf " + germlineVcf} \
+        ~{"-germline_hotspots " + germlineHotspots} \
+        ~{"-germline_del_freq_file " + germlineDelFreqFile} \
         -tumor ~{tumorName} \
         -output_dir ~{outputDir} \
         -amber ~{sub(amberOutput[0], basename(amberOutput[0]), "")} \
@@ -1101,12 +1159,18 @@ task Purple {
         -sv_recovery_vcf ~{fullSvVcf} \
         -circos /usr/local/bin/circos \
         -ref_genome ~{referenceFasta} \
+        -ref_genome_version ~{refGenomeVersion} \
         -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
         -run_drivers \
         -somatic_hotspots ~{somaticHotspots} \
         -driver_gene_panel ~{driverGenePanel} \
         ~{"-highly_diploid_percentage " + highlyDiploidPercentage} \
         ~{"-somatic_min_purity_spread " + somaticMinPuritySpread} \
+        ~{"-target_regions_bed " + targetRegionsBed} \
+        ~{"-target_regions_ratios " + targetRegionsRatios} \
+        ~{"-target_regions_msi_indels " + targetRegionsMsiIndels} \
+        ~{"-min_diploid_tumor_ratio_count " + minDiploidTumorRatioCount} \
+        ~{"-min_diploid_tumor_ratio_count_centromere" + minDiploidTumorRatioCountCentromere} \
         -threads ~{threads}
     }
 
@@ -1153,7 +1217,8 @@ task Purple {
             purpleCnvSomaticTsv, purplePurityRangeTsv, purplePurityTsv, purpleQc,
             purpleSegmentTsv, purpleSomaticClonalityTsv, purpleSomaticHistTsv,
             purpleSomaticVcf, purpleSomaticVcfIndex, purpleSvVcf, purpleSvVcfIndex,
-            purpleVersion, purpleGermlineVcf, purpleGermlineVcfIndex, driverCatalogGermlineTsv]
+            purpleVersion, purpleGermlineVcf, purpleGermlineVcfIndex, driverCatalogGermlineTsv,
+            purpleGermlineDeletionTsv]
         Array[File] plots = select_all([circosPlot, copynumberPlot, inputPlot, mapPlot, purityRangePlot,
             segmentPlot, somaticClonalityPlot, somaticPlot, somaticRainfallPlot])
         Array[File] circos = [circosNormalRatio, circosConf, circosIndel, circosLink,
@@ -1204,72 +1269,163 @@ task Purple {
     }
 }
 
-task Sage {
+task Rose {
     input {
+        File actionabilityDatabaseTsv
+        Boolean hg38 = false
+        File driverGeneTsv
+        File purplePurityTsv
+        File purpleQc
+        File purpleGeneCopyNumberTsv
+        File purpleSomaticDriverCatalogTsv
+        File purpleGermlineDriverCatalogTsv
+        File purpleSomaticVcf
+        File purpleSomaticVcfIndex
+        File purpleGermlineVcf
+        File purpleGermlineVcfIndex
+        File linxFusionTsv
+        File linxBreakendTsv
+        File linxDriverCatalogTsv
+        File annotatedVirusTsv
+        File chordPredictionTxt
+        File cuppaResultCsv
+        String outputDir = "./rose"
         String tumorName
-        File tumorBam
-        File tumorBamIndex
+        String referenceName
+
+        String memory = "9GiB"
+        String javaXmx = "8G"
+        Int timeMinutes = 60
+        String dockerImage = "quay.io/biocontainers/hmftools-rose:1.3--hdfd78af_0"
+    }
+
+    command {
+        set -e
+        mkdir -p ~{outputDir}
+        rose -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        -actionability_database_tsv ~{actionabilityDatabaseTsv} \
+        -ref_genome_version ~{if hg38 then "38" else "37"} \
+        -driver_gene_tsv ~{driverGeneTsv} \
+        -purple_purity_tsv ~{purplePurityTsv} \
+        -purple_qc_file ~{purpleQc} \
+        -purple_gene_copy_number_tsv ~{purpleGeneCopyNumberTsv} \
+        -purple_somatic_driver_catalog_tsv ~{purpleSomaticDriverCatalogTsv} \
+        -purple_germline_driver_catalog_tsv ~{purpleGermlineDriverCatalogTsv} \
+        -purple_somatic_variant_vcf ~{purpleSomaticVcf} \
+        -purple_germline_variant_vcf ~{purpleGermlineVcf} \
+        -linx_fusion_tsv ~{linxFusionTsv} \
+        -linx_breakend_tsv ~{linxBreakendTsv} \
+        -linx_driver_catalog_tsv ~{linxDriverCatalogTsv} \
+        -annotated_virus_tsv ~{annotatedVirusTsv} \
+        -chord_prediction_txt ~{chordPredictionTxt} \
+        -cuppa_result_csv ~{cuppaResultCsv} \
+        -output_dir ~{outputDir} \
+        -tumor_sample_id ~{tumorName} \
+        -ref_sample_id ~{referenceName} \
+        -patient_id not_used_because_primary_tumor_tsv_has_only_headers
+    }
+
+    output {
+        File roseTsv = "~{outputDir}/~{tumorName}.rose.tsv"
+    }
+
+    runtime {
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+        memory: memory
+    }
+
+    parameter_meta {
+
+    }
+}
+
+task Sage {
+    input {
+        Array[String]+ tumorName
+        Array[File]+ tumorBam
+        Array[File]+ tumorBamIndex
         File referenceFasta
         File referenceFastaDict
         File referenceFastaFai
         File hotspots
         File panelBed
         File highConfidenceBed
+        File coverageBed
         Boolean hg38 = false
         Boolean panelOnly = false
         String outputPath = "./sage.vcf.gz"
+        #The following should be in the same directory.
+        File geneDataCsv
+        File proteinFeaturesCsv
+        File transExonDataCsv
+        File transSpliceDataCsv
 
-        String? referenceName
-        File? referenceBam
-        File? referenceBamIndex
+        Array[String] referenceName = []
+        Array[File] referenceBam = []
+        Array[File] referenceBamIndex = []
         Int? hotspotMinTumorQual
         Int? panelMinTumorQual
         Int? hotspotMaxGermlineVaf
         Int? hotspotMaxGermlineRelRawBaseQual
         Int? panelMaxGermlineVaf
         Int? panelMaxGermlineRelRawBaseQual
-        String? mnvFilterEnabled
-        File? coverageBed
+        Int? refSampleCount
+        Float? hotspotMinTumorVaf
+        Int? highConfidenceMinTumorQual
+        Int? lowConfidenceMinTumorQual
 
         Int threads = 32
         String javaXmx = "16G"
         String memory = "20GiB"
         Int timeMinutes = 720
-        String dockerImage = "quay.io/biocontainers/hmftools-sage:2.8--hdfd78af_1"
+        String dockerImage = "quay.io/biocontainers/hmftools-sage:3.2.3--hdfd78af_0"
     }
 
     command {
         SAGE -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-        -tumor ~{tumorName} \
-        -tumor_bam ~{tumorBam} \
-        ~{"-reference " + referenceName} \
-        ~{"-reference_bam " + referenceBam} \
-        -ref_genome ~{referenceFasta} \
+        -tumor ~{sep="," tumorName} \
+        -tumor_bam ~{sep="," tumorBam} \
+        ~{if length(referenceName) > 0 then "-reference" else ""} ~{sep="," referenceName} \
+        ~{if length(referenceBam) > 0 then "-reference_bam" else ""}  ~{sep="," referenceBam} \
         -hotspots ~{hotspots} \
-        -panel_bed ~{panelBed} \
-        -high_confidence_bed ~{highConfidenceBed} \
-        -assembly ~{true="hg38" false="hg19" hg38} \
         ~{"-hotspot_min_tumor_qual " + hotspotMinTumorQual} \
+        -high_confidence_bed ~{highConfidenceBed} \
+        -panel_bed ~{panelBed} \
+        -coverage_bed ~{coverageBed} \
+        -ref_genome ~{referenceFasta} \
+        -ref_genome_version ~{true="38" false="37" hg38} \
+        -ensembl_data_dir ~{sub(geneDataCsv, basename(geneDataCsv), "")} \
+        -write_bqr_data \
+        -write_bqr_plot \
+        -out ~{outputPath} \
+        -threads ~{threads} \
         ~{"-panel_min_tumor_qual " + panelMinTumorQual} \
         ~{"-hotspot_max_germline_vaf " + hotspotMaxGermlineVaf} \
         ~{"-hotspot_max_germline_rel_raw_base_qual " + hotspotMaxGermlineRelRawBaseQual} \
         ~{"-panel_max_germline_vaf " + panelMaxGermlineVaf} \
         ~{"-panel_max_germline_rel_raw_base_qual " + panelMaxGermlineRelRawBaseQual} \
-        ~{"-mnv_filter_enabled " + mnvFilterEnabled} \
-        ~{"-coverage_bed " + coverageBed} \
         ~{true="-panel_only" false="" panelOnly} \
-        -threads ~{threads} \
-        -out ~{outputPath}
+        ~{"-ref_sample_count " + refSampleCount} \
+        ~{"-hotspot_min_tumor_vaf " + hotspotMinTumorVaf} \
+        ~{"-high_confidence_min_tumor_qual " + highConfidenceMinTumorQual} \
+        ~{"-low_confidence_min_tumor_qual " + lowConfidenceMinTumorQual}
     }
 
-    output {
+    String outputDir = sub(outputPath, basename(outputPath), "")
+
+    output { #FIXME does it produce multiple plots/tsvs if multiple samples are given?
         File outputVcf = outputPath
         File outputVcfIndex = outputPath + ".tbi"
-        File? referenceSageBqrPng = "~{referenceName}.sage.bqr.png"
-        File? referenceSageBqrTsv = "~{referenceName}.sage.bqr.tsv"
-        File tumorSageBqrPng = "~{tumorName}.sage.bqr.png"
-        File tumorSageBqrTsv = "~{tumorName}.sage.bqr.tsv"
-        File sageGeneCoverageTsv = "~{tumorName}.sage.gene.coverage.tsv"
+        File? referenceSageBqrPng = "~{outputDir}/~{referenceName[0]}.sage.bqr.png"
+        File? referenceSageBqrTsv = "~{outputDir}/~{referenceName[0]}.sage.bqr.tsv"
+        File tumorSageBqrPng = "~{outputDir}/~{tumorName[0]}.sage.bqr.png"
+        File tumorSageBqrTsv = "~{outputDir}/~{tumorName[0]}.sage.bqr.tsv"
+        File sageGeneCoverageTsv = "~{outputDir}/~{tumorName[0]}.sage.gene.coverage.tsv"
+        File referenceSageExonMediansTsv = "~{outputDir}/~{tumorName[0]}.sage.exon.medians.tsv"
+        Array[File] outputs = select_all([outputVcf, outputVcfIndex, referenceSageBqrPng,
+                                          referenceSageBqrTsv, tumorSageBqrPng, tumorSageBqrTsv,
+                                          sageGeneCoverageTsv, referenceSageExonMediansTsv])
     }
 
     runtime {
@@ -1299,8 +1455,193 @@ task Sage {
         hotspotMaxGermlineRelRawBaseQual: {description: "Equivalent to sage's `hotspot_max_germline_rel_raw_base_qual` option.", category: "advanced"}
         panelMaxGermlineVaf: {description: "Equivalent to sage's `panel_max_germline_vaf` option.", category: "advanced"}
         panelMaxGermlineRelRawBaseQual: {description: "Equivalent to sage's `panel_max_germline_vaf` option.", category: "advanced"}
-        mnvFilterEnabled: {description: "Equivalent to sage's `mnv_filter_enabled` option.", category: "advanced"}
+        refSampleCount: {description: "Equivalent to sage's `ref_sample_count` option.", category: "advanced"}
+        hg38: {description: "Whether or not the refernce genome is HG18, if false HG19 is assumed.", category: "common"}
 
+        threads: {description: "The numve of threads to 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 Sigs {
+    input {
+        String sampleName
+        File signaturesFile
+        File somaticVcfFile
+        File somaticVcfIndex
+        String outputDir = "./sigs"
+
+        String javaXmx = "4G"
+        String memory = "5GiB"
+        Int timeMinutes = 60
+        String dockerImage = "quay.io/biocontainers/hmftools-sigs:1.1--hdfd78af_0"
+    }
+
+    command {
+        set -e
+        mkdir -p ~{outputDir}
+        sigs -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        -sample ~{sampleName} \
+        -signatures_file ~{signaturesFile} \
+        -somatic_vcf_file ~{somaticVcfFile} \
+        -output_dir ~{outputDir}
+    }
+
+    output {
+        File sigAllocationTsv = "~{outputDir}/~{sampleName}.sig.allocation.tsv"
+        File sigSnvCountsCsv = "~{outputDir}/~{sampleName}.sig.snv_counts.csv"
+    }
+
+    runtime {
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        docker: dockerImage
+        memory: memory
+    }
+
+    parameter_meta {
+
+    }
+}
+
+task SvPrep {
+    # for ref also add tumorJunctionFile
+    input {
+        String sampleName
+        File bamFile
+        File bamIndex
+        File referenceFasta
+        File referenceFastaDict
+        File referenceFastaFai
+        File blacklistBed
+        File knownFusionBed
+        String outputDir = "."
+
+        File? existingJunctionFile
+        Boolean hg38 = false
+
+        Int threads = 10
+        String javaXmx = "48G"
+        String memory = "50GiB"
+        Int timeMinutes = 120
+        String dockerImage = "quay.io/biocontainers/hmftools-sv-prep:1.1--hdfd78af_1"
+    }
+
+    command {
+        set -e
+        SvPrep -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        -sample ~{sampleName} \
+        -bam_file ~{bamFile} \
+        -ref_genome ~{referenceFasta} \
+        -ref_genome_version ~{true="38" false="37" hg38} \
+        -blacklist_bed ~{blacklistBed} \
+        -known_fusion_bed ~{knownFusionBed} \
+        ~{"-existing_junction_file " + existingJunctionFile} \
+        -write_types "JUNCTIONS;BAM;FRAGMENT_LENGTH_DIST" \
+        -output_dir ~{outputDir} \
+        -threads ~{threads}
+        samtools sort -O bam ~{outputDir}/~{sampleName}.sv_prep.bam -o ~{outputDir}/~{sampleName}.sv_prep.sorted.bam
+        samtools index ~{outputDir}/~{sampleName}.sv_prep.sorted.bam
+    }
+
+    output {
+        File preppedBam = "~{outputDir}/~{sampleName}.sv_prep.sorted.bam"
+        File preppedBamIndex = "~{outputDir}/~{sampleName}.sv_prep.sorted.bam.bai"
+        File junctions = "~{outputDir}/~{sampleName}.sv_prep.junctions.csv"
+    }
+
+    runtime {
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        cpu: threads
+        docker: dockerImage
+        memory: memory
+    }
+
+    parameter_meta {
+        sampleName: {description: "The name of the sample.", category: "required"}
+        bamFile: {description: "The BAM file to prepare for SV calling with GRIDSS.", category: "required"}
+        bamIndex: {description: "The index for the BAM file.", 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"}
+        blacklistBed: {description: "Blacklist bed file.", category: "required"}
+        knownFusionBed: {description: "Bed file with known fusion sites", category: "required"}
+        outputDir: {description: "Path to the output directory.", category: "common"}
+        existingJunctionFile: {description: "Junctions file generated by an earlier run of this tool, eg. from a paired sample.", category: "common"}
+        hg38: {description: "Whether or not the refernce genome is HG18, if false HG19 is assumed.", category: "common"}
+
+        threads: {description: "The numve of threads to 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 SvPrepDepthAnnotator {
+    input {
+        File inputVcf
+        File inputVcfIndex
+        Array[File]+ bamFiles
+        Array[File]+ bamIndexes
+        Array[String]+ samples
+        File referenceFasta
+        File referenceFastaDict
+        File referenceFastaFai
+        Boolean hg38 = false
+        String outputVcf = "gridss.depth_annotated.vcf.gz"
+
+        Int threads = 10
+        String javaXmx = "48G"
+        String memory = "50GiB"
+        Int timeMinutes = 240
+        String dockerImage = "quay.io/biocontainers/hmftools-sv-prep:1.1--hdfd78af_0"
+    }
+
+    command {
+        set -e
+        mkdir -p "$(dirname ~{outputVcf})"
+        java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
+        -cp /usr/local/share/hmftools-sv-prep-1.1-0/sv-prep.jar \
+        com.hartwig.hmftools.svprep.depth.DepthAnnotator \
+        -input_vcf ~{inputVcf} \
+        -output_vcf ~{outputVcf} \
+        -samples ~{sep="," samples} \
+        -bam_files ~{sep="," bamFiles} \
+        -ref_genome ~{referenceFasta} \
+        -ref_genome_version ~{if hg38 then "38" else "37"} \
+        -threads ~{threads}
+    }
+
+    output {
+        File vcf = outputVcf
+        File vcfIndex = outputVcf + ".tbi"
+    }
+
+    runtime {
+        time_minutes: timeMinutes # !UnknownRuntimeKey
+        cpu: threads
+        docker: dockerImage
+        memory: memory
+    }
+
+    parameter_meta {
+        samples: {description: "The names of the samples.", category: "required"}
+        bamFiles: {description: "The BAM files.", category: "required"}
+        bamIndexes: {description: "The indexes for the BAM files.", 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"}
+        hg38: {description: "Whether or not the refernce genome is HG18, if false HG19 is assumed.", category: "common"}
+        outputVcf: {description: "The path for the output VCF.", category: "common"}
+
+        threads: {description: "The numve of threads to 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"}
@@ -1328,6 +1669,8 @@ task VirusInterpreter {
     }
 
     command {
+        set -e
+        mkdir -p ~{outputDir}
         virus-interpreter -Xmx~{javaXmx} -XX:ParallelGCThreads=1  \
         -sample_id ~{sampleId} \
         -purple_purity_tsv ~{purplePurityTsv} \
diff --git a/peach.wdl b/peach.wdl
index 7da029d0..9ace8958 100644
--- a/peach.wdl
+++ b/peach.wdl
@@ -30,7 +30,7 @@ task Peach {
         File panelJson
 
         String memory = "2GiB"
-        String dockerImage = "quay.io/biowdl/peach:v1.5"
+        String dockerImage = "quay.io/biowdl/peach@sha256:025dc28fe448256729a6022d4d30deaee8105ab83d123dab9640251985240748"
         Int timeMinutes = 5
     }
 
@@ -41,7 +41,7 @@ task Peach {
         --vcf ~{germlineVcf} \
         --sample_t_id ~{tumorName} \
         --sample_r_id ~{normalName} \
-        --tool_version 1.5 \
+        --tool_version 1.7 \
         --outputdir ~{outputDir} \
         --panel ~{panelJson}
     }
diff --git a/picard.wdl b/picard.wdl
index 6628cf0e..314e0a7b 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -510,6 +510,7 @@ task CollectWgsMetrics {
         Int? minimumMappingQuality
         Int? minimumBaseQuality
         Int? coverageCap
+        File? intervals
 
         String memory = "5GiB"
         String javaXmx = "4G"
@@ -528,7 +529,8 @@ task CollectWgsMetrics {
         OUTPUT=~{outputPath} \
         ~{"MINIMUM_MAPPING_QUALITY=" + minimumMappingQuality} \
         ~{"MINIMUM_BASE_QUALITY=" + minimumBaseQuality} \
-        ~{"COVERAGE_CAP=" + coverageCap}
+        ~{"COVERAGE_CAP=" + coverageCap} \
+        ~{"INTERVALS=" + intervals}
     }
 
     output {
diff --git a/sambamba.wdl b/sambamba.wdl
index be347f94..acf40278 100644
--- a/sambamba.wdl
+++ b/sambamba.wdl
@@ -84,7 +84,7 @@ task Markdup {
         # Added 8192 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
         Int memoryMb = 8192 + sortBufferSize + 2 * ioBufferSize
         # Time minute calculation does not work well for higher number of threads.
-        Int timeMinutes = 1 + ceil(size(inputBams, "GiB") * 25) / threads
+        Int timeMinutes = 1 + ceil(size(inputBams, "GiB") * 35) / threads
         String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
     }
 
@@ -139,6 +139,52 @@ task Markdup {
     }
 }
 
+task Slice {
+    input {
+        File bamFile
+        File bamIndex
+        String outputPath = "./sliced.bam"
+        File regions
+
+        String memory = "8G"
+        Int timeMinutes = 720
+        String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
+    }
+
+    command {
+        set -e
+        mkdir -p "$(dirname ~{outputPath})"
+
+        sambamba slice \
+        -L ~{regions} \
+        -o ~{outputPath} \
+        ~{bamFile}
+        sambamba index ~{outputPath}
+    }
+
+    output {
+        File slicedBam = outputPath
+        File slicedBamIndex = "~{outputPath}.bai"
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        bamIndex: {description: "The input BAM files.", category: "required"}
+        outputPath: {description: "Output directory path + output file.", category: "required"}
+        regions: {description: "Regiosn to get sliced.", category: "required"}
+
+        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"}
+    }
+}
+
 task Sort {
     input {
         File inputBam
diff --git a/samtools.wdl b/samtools.wdl
index fbb445e7..875b9ddb 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -566,7 +566,9 @@ task View {
         File inFile
         String outputFileName = "view.bam"
         Boolean uncompressedBamOutput = false
+        Boolean useIndex = false
 
+        File? inFileIndex
         File? referenceFasta
         Int? includeFilter
         Int? excludeFilter
@@ -589,7 +591,8 @@ task View {
         samtools view -b \
         ~{"-T " + referenceFasta} \
         ~{"-o " + outputFileName} \
-        ~{true="-u " false="" uncompressedBamOutput} \
+        ~{if uncompressedBamOutput then "-u" else ""} \
+        ~{if useIndex then "-M" else ""} \
         ~{"-f " + includeFilter} \
         ~{"-F " + excludeFilter} \
         ~{"-G " + excludeSpecificFilter} \
@@ -617,6 +620,8 @@ task View {
         inFile: {description: "A BAM, SAM or CRAM file.", category: "required"}
         outputFileName: {description: "The location the output BAM file should be written.", category: "common"}
         uncompressedBamOutput: {description: "Equivalent to samtools view's `-u` flag.", category: "advanced"}
+        useIndex: {description: "Equivalent to samtools view's `-M` flag.", category: "advanced"}
+        inFileIndex: {description: "An index for the inFile.", category: "common"}
         referenceFasta: {description: "The reference fasta file also used for mapping.", category: "advanced"}
         includeFilter: {description: "Equivalent to samtools view's `-f` option.", category: "advanced"}
         excludeFilter: {description: "Equivalent to samtools view's `-F` option.", category: "advanced"}