rename

tasks/rename_fastq.wdl

 task rename_fastq {
 
 	File fastq_1_D5
+	String fastq_1_D5_name = sub(basename(fastq_1_D5, "_R1.fastq.gz"), "_R1.fq.gz$", "")
 	File fastq_1_D6
+	String fastq_1_D6_name = sub(basename(fastq_1_D6, "_R1.fastq.gz"), "_R1.fq.gz$", "")
 	File fastq_1_F7
+	String fastq_1_F7_name = sub(basename(fastq_1_F7, "_R1.fastq.gz"), "_R1.fq.gz$", "")
 	File fastq_1_M8
+	String fastq_1_M8_name = sub(basename(fastq_1_M8, "_R1.fastq.gz"), "_R1.fq.gz$", "")
 
 	File fastq_2_D5
+	String fastq_2_D5_name = sub(basename(fastq_2_D5, "_R2.fastq.gz"), "_R2.fq.gz$", "")
 	File fastq_2_D6
+	String fastq_2_D6_name = sub(basename(fastq_2_D6, "_R2.fastq.gz"), "_R2.fq.gz$", "")
 	File fastq_2_F7
+	String fastq_2_F7_name = sub(basename(fastq_2_F7, "_R2.fastq.gz"), "_R2.fq.gz$", "")
 	File fastq_2_M8
+	String fastq_2_M8_name = sub(basename(fastq_2_M8, "_R2.fastq.gz"), "_R2.fq.gz$", "")
 
 	String project
 	String docker
 	String disk_size
 
 	command <<<
-		mv fastq_1_D5 ${project}_LCL5_R1.fastq.gz
-		mv fastq_1_D6 ${project}_LCL6_R1.fastq.gz
-		mv fastq_1_F7 ${project}_LCL7_R1.fastq.gz
-		mv fastq_1_M8 ${project}_LCL8_R1.fastq.gz
-		mv fastq_2_D5 ${project}_LCL5_R2.fastq.gz
-		mv fastq_2_D6 ${project}_LCL6_R2.fastq.gz
-		mv fastq_2_F7 ${project}_LCL7_R2.fastq.gz
-		mv fastq_2_M8 ${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
 
 	>>>
 
 	}
 
 	output {
-		File fastq_1_D5_renamed = "${project}_LCL5_R1.fastq.gz"
-		File fastq_1_D6_renamed = "${project}_LCL6_R1.fastq.gz"
-		File fastq_1_F7_renamed = "${project}_LCL7_R1.fastq.gz"
-		File fastq_1_M8_renamed = "${project}_LCL8_R1.fastq.gz"
-		File fastq_2_D5_renamed = "${project}_LCL5_R2.fastq.gz"
-		File fastq_2_D6_renamed = "${project}_LCL6_R2.fastq.gz"
-		File fastq_2_F7_renamed = "${project}_LCL7_R2.fastq.gz"
-		File fastq_2_M8_renamed = "${project}_LCL8_R2.fastq.gz"
+		File fastq_1_D5_renamed = "${fastq_1_D5_name}_${project}_LCL5_R1.fastq.gz"
+		File fastq_1_D6_renamed = "${fastq_1_D6_name}_${project}_LCL6_R1.fastq.gz"
+		File fastq_1_F7_renamed = "${fastq_1_F7_name}_${project}_LCL7_R1.fastq.gz"
+		File fastq_1_M8_renamed = "${fastq_1_M8_name}_${project}_LCL8_R1.fastq.gz"
+		File fastq_2_D5_renamed = "${fastq_2_D5_name}_${project}_LCL5_R2.fastq.gz"
+		File fastq_2_D6_renamed = "${fastq_2_D6_name}_${project}_LCL6_R2.fastq.gz"
+		File fastq_2_F7_renamed = "${fastq_2_F7_name}_${project}_LCL7_R2.fastq.gz"
+		File fastq_2_M8_renamed = "${fastq_2_M8_name}_${project}_LCL8_R2.fastq.gz"
 	}
 }

tasks/rename_vcf.wdl

 task rename_vcf {
 
 	File vcf_D5
+	String vcf_D5_name = basename(vcf_D5, ".vcf")
 	File vcf_D6
+	String vcf_D6_name = basename(vcf_D6, ".vcf")
 	File vcf_F7
+	String vcf_F7_name = basename(vcf_F7, ".vcf")
 	File vcf_M8
+	String vcf_M8_name = basename(vcf_M8, ".vcf")
 
 	String project
 	String docker
 	String disk_size
 
 	command <<<
-		mv vcf_D5 ${project}_LCL5.vcf
-		mv vcf_D6 ${project}_LCL6.vcf
-		mv vcf_F7 ${project}_LCL7.vcf
-		mv vcf_M8 ${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 {
 	}
 
 	output {
-		File vcf_D5_renamed = "${project}_LCL5.vcf"
-		File vcf_D6_renamed = "${project}_LCL6.vcf"
-		File vcf_F7_renamed = "${project}_LCL7.vcf"
-		File vcf_M8_renamed = "${project}_LCL8.vcf"
+		File vcf_D5_renamed = "${vcf_D5_name}_${project}_LCL5.vcf"
+		File vcf_D6_renamed = "${vcf_D6_name}_${project}_LCL6.vcf"
+		File vcf_F7_renamed = "${vcf_F7_name}_${project}_LCL7.vcf"
+		File vcf_M8_renamed = "${vcf_M8_name}_${project}_LCL8.vcf"
 	}
 }