rm qualimap from multiqc

tasks/merge_family.wdl

@@ -35,7 +35,7 @@ task merge_family {
 							echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5\tLCL6\tLCL7\tLCL8" > header_name
 							cat $a | grep '##' | cat - header_name > header
 							paste LCL5.body LCL6.body LCL7.body LCL8.body > family.body
-							cat header family.body > ${project}.$rep_a.family.vcf
+							cat header family.body > ${project}_$rep_a.family.vcf
 						fi
 					done
 				done

tasks/multiqc.wdl

@@ -19,16 +19,11 @@ task multiqc {
 		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=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
 		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
 		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
-		for i in ${sep=" " zip}
-		do
-		  tar -zxvf $i -C /cromwell_root/tmp/bamqc
-		done
 
 		multiqc /cromwell_root/tmp/