rename

tasks/rename_fastq.wdl

@@ -24,14 +24,14 @@ task rename_fastq {
 	String disk_size
 
 	command <<<
-		mv fastq_1_D5 ${fastq_1_D5_name}_${project}_LCL5_R1.fastq.gz
-		mv fastq_1_D6 ${fastq_1_D6_name}_${project}_LCL6_R1.fastq.gz
-		mv fastq_1_F7 ${fastq_1_F7_name}_${project}_LCL7_R1.fastq.gz
-		mv fastq_1_M8 ${fastq_1_M8_name}_${project}_LCL8_R1.fastq.gz
-		mv fastq_2_D5 ${fastq_2_D5_name}_${project}_LCL5_R2.fastq.gz
-		mv fastq_2_D6 ${fastq_2_D6_name}_${project}_LCL6_R2.fastq.gz
-		mv fastq_2_F7 ${fastq_2_F7_name}_${project}_LCL7_R2.fastq.gz
-		mv fastq_2_M8 ${fastq_2_M8_name}_${project}_LCL8_R2.fastq.gz
+		mv ${fastq_1_D5} ${fastq_1_D5_name}_${project}_LCL5_R1.fastq.gz
+		mv ${fastq_1_D6} ${fastq_1_D6_name}_${project}_LCL6_R1.fastq.gz
+		mv ${fastq_1_F7} ${fastq_1_F7_name}_${project}_LCL7_R1.fastq.gz
+		mv ${fastq_1_M8} ${fastq_1_M8_name}_${project}_LCL8_R1.fastq.gz
+		mv ${fastq_2_D5} ${fastq_2_D5_name}_${project}_LCL5_R2.fastq.gz
+		mv ${fastq_2_D6} ${fastq_2_D6_name}_${project}_LCL6_R2.fastq.gz
+		mv ${fastq_2_F7} ${fastq_2_F7_name}_${project}_LCL7_R2.fastq.gz
+		mv ${fastq_2_M8} ${fastq_2_M8_name}_${project}_LCL8_R2.fastq.gz
 
 	>>>
 

tasks/rename_vcf.wdl

@@ -15,10 +15,10 @@ task rename_vcf {
 	String disk_size
 
 	command <<<
-		mv vcf_D5 ${vcf_D5_name}_${project}_LCL5.vcf
-		mv vcf_D6 ${vcf_D6_name}_${project}_LCL6.vcf
-		mv vcf_F7 ${vcf_F7_name}_${project}_LCL7.vcf
-		mv vcf_M8 ${vcf_M8_name}_${project}_LCL8.vcf
+		mv ${vcf_D5} ${vcf_D5_name}_${project}_LCL5.vcf
+		mv ${vcf_D6} ${vcf_D6_name}_${project}_LCL6.vcf
+		mv ${vcf_F7} ${vcf_F7_name}_${project}_LCL7.vcf
+		mv ${vcf_M8} ${vcf_M8_name}_${project}_LCL8.vcf
 	>>>
 
 	runtime {