[refs #119] Adds GATK v3.8 of MuTect2

mutect/MuTect2.wdl

@@ -0,0 +1,94 @@
+version 1.0
+# -------------------------------------------------------------------------------------------------
+# Package Name: MuTect v2, GATK v3.8.1
+# Task Summary: Call somatic SNPs and indels via local re-assembly of haplotypes
+# Tool Name: MuTect2
+# -------------------------------------------------------------------------------------------------
+
+
+task MuTect2 {
+  input {
+    File ? java
+    File gatk
+
+    File tumor_bam
+    File tumor_bam_idx
+    String sample_id
+
+    File ? normal_bam
+    File ? normal_bam_idx
+    String ? normal_sample_id
+
+    Array[File] intervals = []
+    Array[File] germline_resources = []
+
+    File reference
+    File reference_idx
+    File reference_dict
+
+    File ? panel_of_normals
+    String ? userString
+
+    Array[String] modules = []
+    Float memory = 64
+    Int cpu = 16
+  }
+
+  String output_vcf_name = sample_id + '.MuTect2.vcf'
+  Array[String] intervalOptions = prefix("--intervals ", intervals)
+  Array[String] germline_resourceOptions = prefix("--germline-resource ", germline_resources)
+
+  command {
+    set -Eeuxo pipefail;
+
+    for MODULE in ~{sep=' ' modules}; do
+      module load $MODULE
+    done;
+
+    ~{default="java" java} -jar ~{gatk}
+      -T MuTect2 \
+      -R ~{reference} \
+      -I:tumor ~{tumor_bam} \
+      ~{sep=" " intervalOptions} \
+      ~{sep=" " germline_resourceOptions} \
+      ~{"-I:normal " + normal_bam} \
+      ~{userString} \
+      ~{"--panel-of-normals " + panel_of_normals} \
+      -o ~{output_vcf_name};
+  }
+
+  output {
+    File vcf_file = "~{output_vcf_name}"
+    File vcf_idx_file = "~{output_vcf_name}" + ".idx"
+  }
+
+  runtime {
+    memory: memory * 1.5 + " GB"
+    cpu: cpu
+  }
+
+  parameter_meta {
+    gatk: "GATK <v4.0.0 jar file"
+    reference: "Reference sequence file."
+    reference_idx: "Reference sequence index (.fai)."
+    reference_dict: "Reference sequence dict (.dict)."
+    tumor_bam: "BAM file for tumor sample; required."
+    sample_id: "ID for the tumor_bam."
+    normal_bam: "BAM file for normal sample; not required"
+    normal_sample_id: "ID for the normal sample; required if normal_bam is provided"
+    panel_of_normals: "VCF built with MuTect2 CreateSomaticPanelOfNormals"
+    germline_resources: "VCF of other germline events, e.g. gnomAD, dbSNP, COSMIC, etc"
+    intervals: "One or more genomic intervals over which to operate."
+    sample_id: "tumor sample id; prefix for output files"
+    userString: "An optional parameter which allows the user to specify additions to the command line at run time."
+    memory: "GB of RAM to use at runtime."
+    cpu: "Number of CPUs to use at runtime."
+  }
+
+  meta {
+    author: "Mark Welsh"
+    email: "[email protected]"
+    gatk_version: "3.8.1"
+    version: "0.1.0"
+  }
+}