[refs #119] Separate task for strelka2 snvs+indels

GATK now required

strelka/strelka2-snvs-indels.wdl

@@ -0,0 +1,88 @@
+version 1.0
+# -------------------------------------------------------------------------------------------------
+# Package Name: https://github.com/Illumina/strelka
+# Task Summary: fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs
+# Tool Name: Strelka2
+# Documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
+# Example: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md#somatic-configuration-example
+# -------------------------------------------------------------------------------------------------
+
+
+task Strelka2Merged {
+  input {
+    File ? python
+    File ? gatk
+    String strelka2
+
+    File tumor_input
+    File tumor_input_idx
+    File ? normal_input
+    File ? normal_input_idx
+
+    File ? bed_file_bgzip
+    File ? bed_file_idx
+    File reference
+    File reference_idx
+    File reference_dict
+
+    String sample_id
+    String ? userString
+
+    Array[String] modules = []
+    Float memory = 16
+    Int cpu = 4
+  }
+
+  Int pymem = round(memory)
+
+  command {
+    set -Eeuxo pipefail;
+
+    for MODULE in ~{sep=' ' modules}; do
+      module load $MODULE
+    done;
+
+    ~{default="python" python} ~{strelka2} \
+      ~{"--normalBam " + normal_input} \
+      --tumorBam ~{tumor_input} \
+      --referenceFasta ~{reference} \
+      ~{"--callRegions " + bed_file_bgzip} \
+      ~{userString} \
+      --runDir strelka2_run;
+
+    ~{default="python" python} strelka2_run/runWorkflow.py \
+      --mode local \
+      --jobs ~{cpu} \
+      --memGb ~{pymem};
+
+    ~{default="gatk" gatk} MergeVcfs \
+      --SEQUENCE_DICTIONARTY ~{reference_dict} \
+      -I strelka2_run/results/variants/somatic.snvs.vcf.gz -I strelka2_run/results/variants/somatic.indels.vcf.gz \
+      --OUTPUT strelka2_run/results/variants/~{sample_id}.strelka2.somatic.merged.vcf.gz
+  }
+
+  output {
+    File vcf_file = "strelka2_run/results/variants/" + "~{sample_id}" + ".strelka2.somatic.merged.vcf.gz"
+  }
+
+  runtime {
+    memory: memory + " GB"
+    cpu: cpu
+  }
+
+  parameter_meta {
+    python: "Path to Python binary"
+    strelka2: "Path to strelka2 Python script"
+    bed_file_bgzip: "ROI in BED file format that has been BgZip'd"
+    bed_file_idx: "BgZip'd BED file indexed with Tabix"
+    reference: "FASTA reference file"
+    reference_idx: "FASTA reference fil index (.fai)"
+  }
+
+  meta {
+    author: "Mark Welsh"
+    email: "[email protected]"
+    strelka2_verison: "2.9.10"
+    version: "0.2.0"
+  }
+}