multiqc

tasks/multiqc.wdl

 	Array[File] txt1
 	Array[File] txt2
 
-	Array[File] zip
 	Array[File] summary
 
 	String docker
 		set -e
 		mkdir -p /cromwell_root/tmp/fastqc
 		mkdir -p /cromwell_root/tmp/fastqscreen
-		mkdir -p /cromwell_root/tmp/bamqc
 		mkdir -p /cromwell_root/tmp/benchmark
 
 		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
 		cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
 		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
-		for i in ${sep=" " zip}
-		do
-		  tar -zxvf $i -C /cromwell_root/tmp/bamqc
-		done
-
-		multiqc /cromwell_root/tmp/
 
 		cat multiqc_data/multiqc_general_stats.txt > multiqc_general_stats.txt
 		cat multiqc_data/multiqc_fastq_screen.txt > multiqc_fastq_screen.txt