readme

tasks/multiqc.wdl

@@ -24,15 +24,14 @@ task multiqc {
 
 		cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
 		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
-		cp ${sep=" " zip} /cromwell_root/tmp/bamqc
 		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
-		for i in `ls /cromwell_root/tmp/bamqc`
+		for i in ${sep=" " zip}
 		do
 		  tar -zxvf $i -C /cromwell_root/tmp/bamqc
 		done
 
 		multiqc /cromwell_root/tmp/
-		ls > filelist
+	
 	>>>
 
 	runtime {
@@ -43,7 +42,6 @@ task multiqc {
 	}
 
 	output {
-		File filelist = "filelist"
 		File multiqc_html = "multiqc_report.html"
 		Array[File] multiqc_txt = glob("multiqc_data/*")
 	}