......

tasks/fastqc.wdl

@@ -13,8 +13,6 @@ task fastqc {
 		nt=$(nproc)
 		fastqc -t $nt -o ./ ${read1}
 		fastqc -t $nt -o ./ ${read2}
-		tar -zcvf ${bamname1}_fastqc.zip ${bamname1}_fastqc
-		tar -zcvf ${bamname2}_fastqc.zip ${bamname2}_fastqc
 	>>>
 
 	runtime {
@@ -24,8 +22,6 @@ task fastqc {
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		Array[File] fastqc1 = glob("${bamname1}_fastqc/*")
-		Array[File] fastqc2 = glob("${bamname2}_fastqc/*")
 		File read1_html = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html")
 		File read1_zip = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.zip")
 		File read2_html = sub(basename(read2), "\\.(fastq|fq)\\.gz$", "_fastqc.html")

tasks/qualimapBAMqc.wdl

@@ -10,7 +10,7 @@ task qualimapBAMqc {
 		set -e
 		nt=$(nproc)
 		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
-		tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc
+		
 	>>>
 
 	runtime {
@@ -22,6 +22,6 @@ task qualimapBAMqc {
 
 	output {
 		File bamqc_zip = "${bamname}_bamqc_qualimap.zip"
-		Array[File] bamqc = glob("${bamname}_bamqc/*")
+		
 	}
 }

tasks/qualimapRNAseq.wdl

@@ -11,7 +11,7 @@ task qualimapRNAseq {
 		set -e
 		nt=$(nproc)
 		/opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_RNAseq -gtf ${gtf} -pe --java-mem-size=10G
-		tar -zcvf ${bamname}_RNAseq_qualimap.zip ${bamname}_RNAseq
+		
 	>>>
 
 	runtime {
@@ -23,6 +23,6 @@ task qualimapRNAseq {
 
 	output {
 		File rnaseq_zip = "${bamname}_RNAseq_qualimap.zip"
-		Array[File] RNAseqqc = glob("${bamname}_RNAseq/*")
+		
 	}
 }