更新 'workflow.wdl'

workflow.wdl

@@ -57,47 +57,47 @@ workflow {{ project_name }} {
     Boolean AF_filter
 
 
-call MSIsensor.MSIsensor as MSIsensor {
-    input:
-    sample=sample_id,
-    fasta=ref_fasta,
-    ref_dir=ref_fasta_dir,
-    normal_bam=normal_deduped_bam,
-    normal_bam_index=normal_deduped_bam_bai,
-    tumor_bam=tumor_deduped_bam,
-    tumor_bam_index=tumor_deduped_bam_bai,
-    baseline=baseline,
-    docker=docker_MSIsensor,
-    cluster_config=cluster_config,
-    disk_size=disk_size
-  }
-
-
-call Haplotyper.Haplotyper as Haplotyper {
-      input:
-        SENTIEON_LICENSE=SENTIEON_LICENSE,
-        sample=sample_id + '.N',
-        fasta=ref_fasta,
-        ref_dir=ref_fasta_dir,
-        recaled_bam=normal_deduped_bam,
-        recaled_bam_index=normal_deduped_bam_bai,
-        dbsnp=dbsnp,
-        dbsnp_dir=dbsnp_dir,
-        regions=regions,
-        docker=docker_sentieon,
-        disk_size=disk_size,
-        cluster_config=cluster_config
-    }
-
-call bcftools.bcftools as Haplotyper_bcftools {
-      input:
-        vcf=Haplotyper.vcf,
-        fasta=ref_fasta,
-        ref_dir=ref_fasta_dir,
-        docker=docker_bcftools,
-        cluster_config=cluster_config,
-        disk_size=disk_size
-    }
+# call MSIsensor.MSIsensor as MSIsensor {
+#     input:
+#     sample=sample_id,
+#     fasta=ref_fasta,
+#     ref_dir=ref_fasta_dir,
+#     normal_bam=normal_deduped_bam,
+#     normal_bam_index=normal_deduped_bam_bai,
+#     tumor_bam=tumor_deduped_bam,
+#     tumor_bam_index=tumor_deduped_bam_bai,
+#     baseline=baseline,
+#     docker=docker_MSIsensor,
+#     cluster_config=cluster_config,
+#     disk_size=disk_size
+#   }
+
+
+# call Haplotyper.Haplotyper as Haplotyper {
+#       input:
+#         SENTIEON_LICENSE=SENTIEON_LICENSE,
+#         sample=sample_id + '.N',
+#         fasta=ref_fasta,
+#         ref_dir=ref_fasta_dir,
+#         recaled_bam=normal_deduped_bam,
+#         recaled_bam_index=normal_deduped_bam_bai,
+#         dbsnp=dbsnp,
+#         dbsnp_dir=dbsnp_dir,
+#         regions=regions,
+#         docker=docker_sentieon,
+#         disk_size=disk_size,
+#         cluster_config=cluster_config
+#     }
+
+# call bcftools.bcftools as Haplotyper_bcftools {
+#       input:
+#         vcf=Haplotyper.vcf,
+#         fasta=ref_fasta,
+#         ref_dir=ref_fasta_dir,
+#         docker=docker_bcftools,
+#         cluster_config=cluster_config,
+#         disk_size=disk_size
+#     }
 
 call TNseq.sentieon_TNseq as sentieon_TNseq{
 	input:
@@ -144,26 +144,26 @@ if (Annovar){
 			disk_size=disk_size
   }
 
-    call tmb.TMB as TMB{
-        input:
-            sample=sample_id,
-            hg38_CDS=hg38_CDS,
-            regions=regions,
-            snpindel_txt=TNseq_ANNOVAR.multianno_txt,
-            docker=docker_tmb,
-            cluster_config=cluster_config,
-            disk_size=disk_size,
-            AF_filter=AF_filter
-    }
-
-    call annovar.ANNOVAR as Haplotyper_ANNOVAR {
-		input:
-			vcf=Haplotyper_bcftools.norm_vcf,
-			annovar_database=annovar_database,
-			docker=docker_annovar,
-			cluster_config=cluster_config,
-			disk_size=disk_size
-  	}
+    # call tmb.TMB as TMB{
+    #     input:
+    #         sample=sample_id,
+    #         hg38_CDS=hg38_CDS,
+    #         regions=regions,
+    #         snpindel_txt=TNseq_ANNOVAR.multianno_txt,
+    #         docker=docker_tmb,
+    #         cluster_config=cluster_config,
+    #         disk_size=disk_size,
+    #         AF_filter=AF_filter
+    # }
+
+    # call annovar.ANNOVAR as Haplotyper_ANNOVAR {
+	# 	input:
+	# 		vcf=Haplotyper_bcftools.norm_vcf,
+	# 		annovar_database=annovar_database,
+	# 		docker=docker_annovar,
+	# 		cluster_config=cluster_config,
+	# 		disk_size=disk_size
+  	# }