rm

tasks/rename_fastq.wdl

@@ -25,13 +25,21 @@ task rename_fastq {
 
 	command <<<
 		cp ${fastq_1_D5} ${fastq_1_D5_name}_${project}_LCL5_R1.fastq.gz
+		rm ${fastq_1_D5}
 		cp ${fastq_1_D6} ${fastq_1_D6_name}_${project}_LCL6_R1.fastq.gz
+		rm ${fastq_1_D6}
 		cp ${fastq_1_F7} ${fastq_1_F7_name}_${project}_LCL7_R1.fastq.gz
+		rm ${fastq_1_F7}
 		cp ${fastq_1_M8} ${fastq_1_M8_name}_${project}_LCL8_R1.fastq.gz
+		rm ${fastq_1_M8}
 		cp ${fastq_2_D5} ${fastq_2_D5_name}_${project}_LCL5_R2.fastq.gz
+		rm ${fastq_2_D5}
 		cp ${fastq_2_D6} ${fastq_2_D6_name}_${project}_LCL6_R2.fastq.gz
+		rm ${fastq_2_D6}
 		cp ${fastq_2_F7} ${fastq_2_F7_name}_${project}_LCL7_R2.fastq.gz
+		rm ${fastq_2_F7}
 		cp ${fastq_2_M8} ${fastq_2_M8_name}_${project}_LCL8_R2.fastq.gz
+		rm ${fastq_2_M8}
 
 	>>>
 

tasks/rename_vcf.wdl

@@ -16,9 +16,13 @@ task rename_vcf {
 
 	command <<<
 		cp ${vcf_D5} ${vcf_D5_name}_${project}_LCL5.vcf
+		rm ${vcf_D5}
 		cp ${vcf_D6} ${vcf_D6_name}_${project}_LCL6.vcf
+		rm ${vcf_D6}
 		cp ${vcf_F7} ${vcf_F7_name}_${project}_LCL7.vcf
+		rm ${vcf_F7}
 		cp ${vcf_M8} ${vcf_M8_name}_${project}_LCL8.vcf
+		rm ${vcf_M8}
 	>>>
 
 	runtime {