multiqc

tasks/multiqc.wdl

@@ -23,6 +23,8 @@ task multiqc {
 		cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
 		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
 
+		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
 		cat multiqc_data/multiqc_happy_data.json > multiqc_happy_data.json