remove multiqc

tasks/multiqc.wdl

@@ -1,50 +0,0 @@
-task multiqc {
-
-	Array[File] read1_zip
-	Array[File] read2_zip
-
-	Array[File] txt1
-	Array[File] txt2
-
-	Array[File] summary
-
-	Array[File] zip
-
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		set -o pipefail
-		set -e
-		mkdir -p /cromwell_root/tmp/fastqc
-		mkdir -p /cromwell_root/tmp/fastqscreen
-		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
-
-		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
-	
-	>>>
-
-	runtime {
-		docker:docker
-		cluster:cluster_config
-		systemDisk:"cloud_ssd 40"
-		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File multiqc_html = "multiqc_report.html"
-		Array[File] multiqc_txt = glob("multiqc_data/*")
-		File fastqc = "multiqc_general_stats.txt"
-		File fastqscreen = "multiqc_fastq_screen.txt"
-		File hap = "multiqc_happy_data.json"
-	}
-}

workflow.wdl

@@ -9,7 +9,6 @@ import "./tasks/Haplotyper_gVCF.wdl" as Haplotyper_gVCF
 import "./tasks/GVCFtyper.wdl" as GVCFtyper
 import "./tasks/split_gvcf_files.wdl" as split_gvcf_files
 import "./tasks/benchmark.wdl" as benchmark
-# import "./tasks/multiqc.wdl" as multiqc
 import "./tasks/merge_sentieon_metrics.wdl" as merge_sentieon_metrics
 import "./tasks/extract_tables.wdl" as extract_tables
 import "./tasks/mendelian.wdl" as mendelian
@@ -222,19 +221,6 @@ workflow {{ project_name }} {
 
 	}
 
-#	call multiqc.multiqc as multiqc {
-#		input:
-#		read1_zip=fastqc.read1_zip,
-#		read2_zip=fastqc.read2_zip,
-#		txt1=fastqscreen.txt1,
-#		txt2=fastqscreen.txt2,
-#		summary=benchmark.summary,
-#		zip=qualimap.zip,
-#		docker=MULTIQCdocker,
-#		cluster_config=SMALLcluster_config,
-#		disk_size=disk_size
-#	}
-
 	call merge_sentieon_metrics.merge_sentieon_metrics as merge_sentieon_metrics {
 		input:
 		quality_yield_header=sentieon.quality_yield_header,