Remove corealigner and vcf2maf

tasks/vcf2maf.wdl

@@ -1,25 +0,0 @@
-task vcf2maf {
-
-	String sample
-	File multianno_txt
-	String maf_name = basename(multianno_txt,".hg38_multianno.txt")
-
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		vcf2maf ${multianno_txt} ${maf_name}.maf
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File maf = "${maf_name}.maf"
-	}
-}

workflow.wdl

@@ -293,15 +293,6 @@ workflow {{ project_name }} {
             cluster_config=cluster_config,
             disk_size=disk_size
         }
-
-        call vcf2maf.vcf2maf as TNseq_vcf2maf {
-            input:
-            sample=sample_id,
-            multianno_txt=TNseq_annovar.multianno_txt,
-            docker=maftools_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
     }
 
     if (tnscope) {
@@ -341,15 +332,6 @@ workflow {{ project_name }} {
             cluster_config=cluster_config,
             disk_size=disk_size
         }
-
-        call vcf2maf.vcf2maf as TNscope_vcf2maf {
-            input:
-            sample=sample_id,
-            multianno_txt=TNscope_annovar.multianno_txt,
-            docker=maftools_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
     }
 
     if (varscan) {
@@ -420,15 +402,6 @@ workflow {{ project_name }} {
             cluster_config=cluster_config,
             disk_size=disk_size
         }
-
-        call vcf2maf.vcf2maf as snp_loh_vcf2maf {
-            input:
-            sample=sample_id,
-            multianno_txt=snp_loh_annovar.multianno_txt,
-            docker=maftools_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
         
         call annovar.annovar as indel_somatic_annovar {
             input: 
@@ -440,15 +413,6 @@ workflow {{ project_name }} {
             disk_size=disk_size
         }
         
-        call vcf2maf.vcf2maf as indel_somatic_vcf2maf {
-            input:
-            sample=sample_id,
-            multianno_txt=indel_somatic_annovar.multianno_txt,
-            docker=maftools_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
-        }
-        
         call annovar.annovar as indel_loh_annovar {
             input: 
             sample=sample_id,
@@ -458,14 +422,6 @@ workflow {{ project_name }} {
             cluster_config=cluster_config,
             disk_size=disk_size
         }
-
-        call vcf2maf.vcf2maf as indel_loh_vcf2maf {
-            input:
-            sample=sample_id,
-            multianno_txt=indel_loh_annovar.multianno_txt,
-            docker=maftools_docker,
-            cluster_config=cluster_config,
-            disk_size=disk_size
         }
     }
 }