Automated integrated analysis software for genomics data of the cancer patients.
Vous ne pouvez pas sélectionner plus de 25 sujets
Les noms de sujets doivent commencer par une lettre ou un nombre, peuvent contenir des tirets ('-') et peuvent comporter jusqu'à 35 caractères.
|
- task processSomatic {
-
- String sample
- File varscan_snp
- File varscan_indel
-
- String docker
- String cluster_config
- String disk_size
-
- command <<<
- cp ${varscan_snp} ./
- cp ${varscan_indel} ./
- java -Xmx32g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf
- java -Xmx32g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf
-
- >>>
-
- runtime {
- docker: docker
- cluster: cluster_config
- systemDisk: "cloud_ssd 40"
- dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
- }
-
- output {
- File varscan_snp_somatic = "${sample}.VarScan.SNP.Somatic.vcf"
- File varscan_snp_germline = "${sample}.VarScan.SNP.Germline.vcf"
- File varscan_snp_loh = "${sample}.VarScan.SNP.LOH.vcf"
- File varscan_snp_somatic_hc = "${sample}.VarScan.SNP.Somatic.hc.vcf"
- File varscan_snp_germline_hc = "${sample}.VarScan.SNP.Germline.hc.vcf"
- File varscan_snp_loh_hc = "${sample}.VarScan.SNP.LOH.hc.vcf"
- File varscan_indel_somatic = "${sample}.VarScan.INDEL.Somatic.vcf"
- File varscan_indel_germline = "${sample}.VarScan.INDEL.Germline.vcf"
- File varscan_indel_loh = "${sample}.VarScan.INDEL.LOH.vcf"
- File varscan_indel_somatic_hc = "${sample}.VarScan.INDEL.Somatic.hc.vcf"
- File varscan_indel_germline_hc = "${sample}.VarScan.INDEL.Germline.hc.vcf"
- File varscan_indel_loh_hc = "${sample}.VarScan.INDEL.LOH.hc.vcf"
- }
- }
|
