Merge pull request #303 from biowdl/sage

Updates for WGSinCancerDiagnostics

CHANGELOG.md

@@ -9,6 +9,19 @@ that users understand how the changes affect the new version.
 -->
 version 5.1.0-dev
 ---------------------------
++ Added a task for CupGenerateReport.
++ Updated Cuppa to version 1.6.
++ Added a task for Gripss.
++ Fixed the HealthChecker task's determination of the `succeeded` output
+  value.
++ Updated Linx to version 1.18.
++ Added a task for LinxVisualization.
++ Added a task for HMFtools Orange.
++ Added a task for HMFtools Pave.
++ Updated Purple to version 3.2.
++ Added plot and table outputs of Sage to task outputs.
++ Updated virus-interpreter to version 1.2.
++ Updated Peach to version 1.5.
 + Added a task to add SVTYPE annotations to GRIDSS results
   (`AnnotateSvTypes`).
 + The GRIDSS task will now run tabix separately if GRIDSS doesn't

peach.wdl

@@ -22,7 +22,6 @@ version 1.0
 
 task Peach {
     input {
-        File transcriptTsv
         File germlineVcf
         File germlineVcfIndex
         String tumorName
@@ -31,28 +30,26 @@ task Peach {
         File panelJson
 
         String memory = "2G"
-        String dockerImage = "quay.io/biowdl/peach:v1.0"
+        String dockerImage = "quay.io/biowdl/peach:v1.5"
         Int timeMinutes = 5
     }
 
     command {
+        set -e
+        mkdir -p ~{outputDir}
         peach \
-        --recreate_bed \
-        --transcript_tsv ~{transcriptTsv} \
-        ~{germlineVcf} \
-        ~{tumorName} \
-        ~{normalName} \
-        1.0 \
-        ~{outputDir} \
-        ~{panelJson} \
-        vcftools
+        --vcf ~{germlineVcf} \
+        --sample_t_id ~{tumorName} \
+        --sample_r_id ~{normalName} \
+        --tool_version 1.5 \
+        --outputdir ~{outputDir} \
+        --panel ~{panelJson}
     }
 
     output {
         File callsTsv = "~{outputDir}/~{tumorName}.peach.calls.tsv"
-        File filteredVcf = "~{outputDir}/~{tumorName}.peach.filtered.vcf"
         File genotypeTsv = "~{outputDir}/~{tumorName}.peach.genotype.tsv"
-        Array[File] outputs = [callsTsv, filteredVcf, genotypeTsv]
+        Array[File] outputs = [callsTsv, genotypeTsv]
     }
 
     runtime {
@@ -62,7 +59,6 @@ task Peach {
     }
 
     parameter_meta {
-        transcriptTsv: {description: "A tsv file describing transcripts.", category: "required"}
         germlineVcf: {description: "The germline VCF file from hmftools' purple.", category: "required"}
         germlineVcfIndex: {description: "The germline VCF's index.", category: "required"}
         tumorName: {description: "The name of the tumor sample.", category: "required"}
@@ -74,4 +70,4 @@ task Peach {
         memory: {description: "The amount of memory available to the job.", category: "advanced"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
     }
-}
+}
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