diff --git a/strelka/strelka2-snvs-indels.wdl b/strelka/strelka2-snvs-indels.wdl new file mode 100644 index 0000000..2f3f61b --- /dev/null +++ b/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: "welshm3@email.chop.edu" + strelka2_verison: "2.9.10" + version: "0.2.0" + } +} diff --git a/strelka/strelka2.wdl b/strelka/strelka2-snvs-only.wdl similarity index 100% rename from strelka/strelka2.wdl rename to strelka/strelka2-snvs-only.wdl