更新 'workflow.wdl'

workflow.wdl

@@ -57,57 +57,15 @@ workflow {{ project_name }} {
     Boolean AF_filter
 
 
-if (normal_deduped_bam != ""){
-
-		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_normal{
-			input:
-				ref_dir=ref_fasta_dir,
-				dbsnp_dir=dbsnp_dir,
-				dbmills_dir = dbmills_dir,
-				sample_id=sample_id+'_N',
-				ref_fasta=ref_fasta,
-				dbsnp=dbsnp,
-				db_mills=db_mills,
-				deduped_bam=normal_deduped_bam,
-				deduped_bam_index=normal_deduped_bam_bai,
-				docker=docker_sentieon,
-				cluster_config=cluster_config,
-				disk_size=disk_size,
-				SENTIEON_LICENSE=SENTIEON_LICENSE
-		}
-
-	}
-
-if (tumor_deduped_bam != ""){
-
-		call Sentieon_BQSR.Sentieon_BQSR as Sentieon_BQSR_tumor{
-			input:
-				ref_dir=ref_fasta_dir,
-				dbsnp_dir=dbsnp_dir,
-				dbmills_dir = dbmills_dir,
-				sample_id=sample_id+'_T',
-				ref_fasta=ref_fasta,
-				dbsnp=dbsnp,
-				db_mills=db_mills,
-				deduped_bam=tumor_deduped_bam,
-				deduped_bam_index=tumor_deduped_bam_bai,
-				docker=docker_sentieon,
-				cluster_config=cluster_config,
-				disk_size=disk_size,
-				SENTIEON_LICENSE=SENTIEON_LICENSE
-		}
-
-	}
-
 call MSIsensor.MSIsensor as MSIsensor {
     input:
     sample=sample_id,
     fasta=ref_fasta,
     ref_dir=ref_fasta_dir,
-    normal_bam=Sentieon_BQSR_normal.recaled_bam,
-    normal_bam_index=Sentieon_BQSR_normal.recaled_bam_index,
-    tumor_bam=Sentieon_BQSR_tumor.recaled_bam,
-    tumor_bam_index=Sentieon_BQSR_tumor.recaled_bam_index,
+    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,
@@ -121,8 +79,8 @@ call Haplotyper.Haplotyper as Haplotyper {
         sample=sample_id + '.N',
         fasta=ref_fasta,
         ref_dir=ref_fasta_dir,
-        recaled_bam=Sentieon_BQSR_normal.recaled_bam,
-        recaled_bam_index=Sentieon_BQSR_normal.recaled_bam_index,
+        recaled_bam=normal_deduped_bam,
+        recaled_bam_index=normal_deduped_bam_bai,
         dbsnp=dbsnp,
         dbsnp_dir=dbsnp_dir,
         regions=regions,
@@ -144,10 +102,10 @@ call bcftools.bcftools as Haplotyper_bcftools {
 call TNseq.sentieon_TNseq as sentieon_TNseq{
 	input:
 		sample_id = sample_id,
-		tumor_bam = Sentieon_BQSR_tumor.recaled_bam,
-		tumor_bam_bai = Sentieon_BQSR_tumor.recaled_bam_index,
-		normal_bam = Sentieon_BQSR_normal.recaled_bam,
-		normal_bam_bai = Sentieon_BQSR_normal.recaled_bam_index,
+		tumor_bam = tumor_deduped_bam,
+		tumor_bam_bai = tumor_deduped_bam_bai,
+		normal_bam = normal_deduped_bam,
+		normal_bam_bai = normal_deduped_bam_bai,
 		tumor_name = sample_id+'_T',
 		normal_name = sample_id+'_N',