remove multiqc

tasks/extract_tables.wdl

@@ -1,41 +0,0 @@
-task extract_tables {
-
-	File quality_yield_summary
-	File wgs_metrics_summary
-	File aln_metrics_summary
-	File is_metrics_summary
-	File hap
-	File fastqc
-	File fastqscreen
-
-
-	String project
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-
-		python /opt/extract_tables.py -quality ${quality_yield_summary} -depth ${wgs_metrics_summary} -aln ${aln_metrics_summary} -is ${is_metrics_summary} -fastqc ${fastqc} -fastqscreen ${fastqscreen} -hap ${hap} -project ${project}
-
-		cat variants.calling.qc.txt | cut -f12- | grep -v 'SNV' | awk '{for(i=1;i<=NF;i++) {sum[i] += $i; sumsq[i] += ($i)^2}} 
-          END {for (i=1;i<=NF;i++) {
-          printf "%f %f \n", sum[i]/NR, sqrt((sumsq[i]-sum[i]^2/NR)/NR)}
-         }' >> reference_datasets_aver-std.txt
-
-	>>>
-
-	runtime {
-		docker:docker
-		cluster:cluster_config
-		systemDisk:"cloud_ssd 40"
-		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File pre_alignment = "pre_alignment.txt"
-		File post_alignment = "post_alignment.txt"
-		File variant_calling = "variants.calling.qc.txt"
-		File precision_recall = "reference_datasets_aver-std.txt"
-	}
-}

workflow.wdl

@@ -10,7 +10,6 @@ import "./tasks/GVCFtyper.wdl" as GVCFtyper
 import "./tasks/split_gvcf_files.wdl" as split_gvcf_files
 import "./tasks/benchmark.wdl" as benchmark
 import "./tasks/merge_sentieon_metrics.wdl" as merge_sentieon_metrics
-import "./tasks/extract_tables.wdl" as extract_tables
 import "./tasks/mendelian.wdl" as mendelian
 import "./tasks/merge_mendelian.wdl" as merge_mendelian
 import "./tasks/quartet_mendelian.wdl" as quartet_mendelian
@@ -235,18 +234,6 @@ workflow {{ project_name }} {
 		docker=MULTIQCdocker,
 		cluster_config=SMALLcluster_config,
 		disk_size=disk_size	
-	}
-
-	call extract_tables.extract_tables as extract_tables {
-		input:
-		quality_yield_summary=merge_sentieon_metrics.quality_yield_summary,
-		wgs_metrics_summary=merge_sentieon_metrics.wgs_metrics_summary,
-		aln_metrics_summary=merge_sentieon_metrics.aln_metrics_summary,
-		is_metrics_summary=merge_sentieon_metrics.is_metrics_summary,
-		project=project,
-		docker=DIYdocker,
-		cluster_config=SMALLcluster_config,
-		disk_size=disk_size
 	}	
 
 	Boolean sister_tag = read_boolean(split_gvcf_files.sister_tag)