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variant-calling
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Germline & Somatic short variant discovery (SNVs + Indels) for WGS & WES.
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variant-calling/tasks/processSomatic.wdl

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  1. task processSomatic {

  2.     

  3.     String sample

  4.     File varscan_snp

  5.     File varscan_indel

  6.     

  7.     String docker

  8.     String cluster_config

  9.     String disk_size

  10. 

  11.     command <<<

  12.         cp ${varscan_snp} ./

  13.         cp ${varscan_indel} ./

  14.         java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.SNP.vcf

  15.         java -Xmx12g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.TN.INDEL.vcf

  16. 

  17.     >>>

  18. 

  19.     runtime {

  20.         docker: docker

  21.         cluster: cluster_config

  22.         systemDisk: "cloud_ssd 40"

  23.         dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

  24.     }

  25. 

  26.     output {

  27.         File varscan_snp_somatic = "${sample}.VarScan.TN.SNP.Somatic.vcf"

  28.         File varscan_snp_germline = "${sample}.VarScan.TN.SNP.Germline.vcf"

  29.         File varscan_snp_loh = "${sample}.VarScan.TN.SNP.LOH.vcf"

  30.         File varscan_snp_somatic_hc = "${sample}.VarScan.TN.SNP.Somatic.hc.vcf"

  31.         File varscan_snp_germline_hc = "${sample}.VarScan.TN.SNP.Germline.hc.vcf"

  32.         File varscan_snp_loh_hc = "${sample}.VarScan.TN.SNP.LOH.hc.vcf"

  33.         File varscan_indel_somatic = "${sample}.VarScan.TN.INDEL.Somatic.vcf"

  34.         File varscan_indel_germline = "${sample}.VarScan.TN.INDEL.Germline.vcf"

  35.         File varscan_indel_loh = "${sample}.VarScan.TN.INDEL.LOH.vcf"

  36.         File varscan_indel_somatic_hc = "${sample}.VarScan.TN.INDEL.Somatic.hc.vcf"

  37.         File varscan_indel_germline_hc = "${sample}.VarScan.TN.INDEL.Germline.hc.vcf"

  38.         File varscan_indel_loh_hc = "${sample}.VarScan.TN.INDEL.LOH.hc.vcf"

  39.     }

  40. }