test16

README.md

@@ -10,12 +10,6 @@
 
 ## Install
 
-```
-open-choppy-env
-choppy install renluyao/quartet_dna_quality_control_big_pipeline
-```
-## Usage
-
 ```
 open-choppy-env
 choppy install renluyao/quartet_dna_quality_control_big_pipeline

workflow.wdl

@@ -69,10 +69,10 @@ workflow {{ project_name }} {
 	String SMALLcluster_config
 
 	# Fastq is not null, which means starting from fastq
-	if (defined(fastq_1_D5) && defined(fastq_2_D5) 
-		&& defined(fastq_1_D6) && defined(fastq_2_D6)
-		&& defined(fastq_1_F7) && defined(fastq_2_F7)
-		&& defined(fastq_1_M8) && defined(fastq_2_M8)) {
+	if (fastq_1_D5 != "" && fastq_2_D5 != ""
+		&& fastq_1_D6 != "" && fastq_2_D6 != ""
+		&& fastq_1_F7 != "" && fastq_2_F7 != ""
+		&& fastq_1_M8 != "" && fastq_2_M8 != "") {
 
 		call mapping.mapping as mapping_D5 {
 			input: 
@@ -732,7 +732,7 @@ workflow {{ project_name }} {
 	} 
 	
 	# Fastq is null, check if starts with vcf
-	if (defined(vcf_D5) && defined(vcf_D6) && defined(vcf_F7) && defined(vcf_M8) ) {
+	if (vcf_D5 != "" && vcf_D6 != "" && vcf_F7 != "" && vcf_M8 != "" ) {
 		call rename_vcf.rename_vcf as rename_vcf{
 			input:
 			vcf_D5=vcf_D5,