|
- task rename_vcf {
-
- File vcf_D5
- String vcf_D5_name = basename(vcf_D5, ".vcf")
- File vcf_D6
- String vcf_D6_name = basename(vcf_D6, ".vcf")
- File vcf_F7
- String vcf_F7_name = basename(vcf_F7, ".vcf")
- File vcf_M8
- String vcf_M8_name = basename(vcf_M8, ".vcf")
-
- String project
- String docker
- String cluster_config
- String disk_size
-
- command <<<
- cp ${vcf_D5} ${vcf_D5_name}_${project}_LCL5.vcf
- cp ${vcf_D6} ${vcf_D6_name}_${project}_LCL6.vcf
- cp ${vcf_F7} ${vcf_F7_name}_${project}_LCL7.vcf
- cp ${vcf_M8} ${vcf_M8_name}_${project}_LCL8.vcf
- # cp ${vcf_D5} vcf_D5.vcf.gz
- # cp ${vcf_D6} vcf_D6.vcf.gz
- # cp ${vcf_F7} vcf_F7.vcf.gz
- # cp ${vcf_M8} vcf_M8.vcf.gz
- # gunzip vcf_D5.vcf.gz > ${vcf_D5_name}_${project}_LCL5.vcf
- # gunzip vcf_D6.vcf.gz > ${vcf_D6_name}_${project}_LCL6.vcf
- # gunzip vcf_F7.vcf.gz > ${vcf_F7_name}_${project}_LCL7.vcf
- # gunzip vcf_M8.vcf.gz > ${vcf_M8_name}_${project}_LCL8.vcf
- >>>
-
- runtime {
- docker:docker
- cluster:cluster_config
- systemDisk:"cloud_ssd 40"
- dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
- }
-
- output {
- File vcf_D5_renamed = "${vcf_D5_name}_${project}_LCL5.vcf"
- File vcf_D6_renamed = "${vcf_D6_name}_${project}_LCL6.vcf"
- File vcf_F7_renamed = "${vcf_F7_name}_${project}_LCL7.vcf"
- File vcf_M8_renamed = "${vcf_M8_name}_${project}_LCL8.vcf"
- }
- }
|
