rename

tasks/fastqc.wdl

 	String docker
 	String project
 	String sample
+	String user_define_name = sub(basename(read1, "_R1.fastq.gz"), "_R1.fq.gz$", "")
 	String cluster_config
 	String disk_size
 
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		cp ${read1} ${project}_${sample}_R1.fastq.gz
-		cp ${read2} ${project}_${sample}_R2.fastq.gz
-		fastqc -t $nt -o ./ ${project}_${sample}_R1.fastq.gz
-		fastqc -t $nt -o ./ ${project}_${sample}_R2.fastq.gz
+		cp ${read1} ${user_define_name}_${project}_${sample}_R1.fastq.gz
+		cp ${read2} ${user_define_name}_${project}_${sample}_R2.fastq.gz
+		fastqc -t $nt -o ./ ${user_define_name}_${project}_${sample}_R1.fastq.gz
+		fastqc -t $nt -o ./ ${user_define_name}_${project}_${sample}_R2.fastq.gz
 	>>>
 
 	runtime {
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File read1_html = "${project}_${sample}_R1_fastqc.html"
-		File read1_zip = "${project}_${sample}_R1_fastqc.zip"
-		File read2_html = "${project}_${sample}_R2_fastqc.html"
-		File read2_zip = "${project}_${sample}_R2_fastqc.html"
+		File read1_html = "${user_define_name}_${project}_${sample}_R1_fastqc.html"
+		File read1_zip = "${user_define_name}_${project}_${sample}_R1_fastqc.zip"
+		File read2_html = "${user_define_name}_${project}_${sample}_R2_fastqc.html"
+		File read2_zip = "${user_define_name}_${project}_${sample}_R2_fastqc.html"
 	}
 }

tasks/fastqscreen.wdl

 	File fastq_screen_conf
 	String docker
 	String project
+	String user_define_name = sub(basename(read1, "_R1.fastq.gz"), "_R1.fq.gz$", "")
 	String sample
 	String cluster_config
 	String disk_size
 		nt=$(nproc)
 		mkdir -p /cromwell_root/tmp
 		cp -r ${screen_ref_dir} /cromwell_root/tmp/
-		cp ${read1} ${project}_${sample}_R1.fastq.gz
-		cp ${read2} ${project}_${sample}_R2.fastq.gz
-		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${project}_${sample}_R1.fastq.gz
-		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${project}_${sample}_R2.fastq.gz
+		cp ${read1} ${user_define_name}_${project}_${sample}_R1.fastq.gz
+		cp ${read2} ${user_define_name}_${project}_${sample}_R2.fastq.gz
+		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${user_define_name}_${project}_${sample}_R1.fastq.gz
+		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --subset 1000000 --threads $nt ${user_define_name}_${project}_${sample}_R2.fastq.gz
 	>>>
 
 	runtime {
 	}
 	
 	output {
-		File png1 = "${project}_${sample}_R1_screen.png"
-		File txt1 = "${project}_${sample}_R1_screen.txt"
-		File html1 = "${project}_${sample}_R1_screen.html"
-		File png2 = "${project}_${sample}_R2_screen.png"
-		File txt2 = "${project}_${sample}_R2_screen.txt"
-		File html2 = "${project}_${sample}_R2_screen.html"
+		File png1 = "${user_define_name}_${project}_${sample}_R1_screen.png"
+		File txt1 = "${user_define_name}_${project}_${sample}_R1_screen.txt"
+		File html1 = "${user_define_name}_${project}_${sample}_R1_screen.html"
+		File png2 = "${user_define_name}_${project}_${sample}_R2_screen.png"
+		File txt2 = "${user_define_name}_${project}_${sample}_R2_screen.txt"
+		File html2 = "${user_define_name}_${project}_${sample}_R2_screen.html"
 	}
 }