更新 'workflow.wdl'

workflow.wdl

@@ -1,4 +1,4 @@
-import "./tasks/fastp.wdl" as fastp
+#import "./tasks/fastp.wdl" as fastp
 import "./tasks/fastqTobam.wdl" as fastqTobam
 import "./tasks/qualimap.wdl" as qualimap
 import "./tasks/BQSR.wdl" as Sentieon_BQSR
@@ -40,25 +40,12 @@ workflow {{ project_name }} {
 	#config
     String cluster_config
     String disk_size
-	Boolean fastqc
+	Boolean? fastqc
 	Boolean bamqc
 
 
 if (normal_in1 != ""){
 	
-	if (fastqc){
-		call fastp.fastp as fastp_normal{
-			input:
-				in1=normal_in1,
-				in2=normal_in2,
-				sample_id=sample_id+'_N',
-				docker=docker_fastp,
-				cluster_config=cluster_config,
-				disk_size=disk_size	
-	
-	} 
-
-	if (!fastqc){
 		call fastqTobam.SentieonFastqToBam as SentieonFastqToBam_normal{
 			input:
 				fastq1=normal_in1,
@@ -109,25 +96,9 @@ if (normal_in1 != ""){
 		}
 
 	}
-	}
-
-}
 
 if (tumor_in1 != ""){
-	
-	if (fastqc){
-		call fastp.fastp as fastp_tumor{
-			input:
-				in1=tumor_in1,
-				in2=tumor_in2,
-				sample_id=sample_id+'_T',
-				docker=docker_fastp,
-				cluster_config=cluster_config,
-				disk_size=disk_size	
-	
-	} 
 
-	if (!fastqc){
 		call fastqTobam.SentieonFastqToBam as SentieonFastqToBam_tumor{
 			input:
 				fastq1=tumor_in1,
@@ -178,9 +149,6 @@ if (tumor_in1 != ""){
 		}
 
 	}
-	}
-
-}
 
 call TNseq.sentieon_TNseq as sentieon_TNseq{
 	input: