split fastq and vcf

inputs

@@ -16,7 +16,6 @@
   "{{ project_name }}.fastq_1_M8": "{{ fastq_1_M8 }}",
   "{{ project_name }}.SMALLcluster_config": "{{ SMALLcluster_config }}",
   "{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
-  "{{ project_name }}.bed": "{{ bed }}",
   "{{ project_name }}.fastq_1_D5": "{{ fastq_1_D5 }}",
   "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
   "{{ project_name }}.BIGcluster_config": "{{ BIGcluster_config }}",

tasks/extract_tables.wdl

@@ -1,12 +1,12 @@
 task extract_tables {
 
-	File? quality_yield_summary
-	File? wgs_metrics_summary
-	File? aln_metrics_summary
-	File? is_metrics_summary
+	File quality_yield_summary
+	File wgs_metrics_summary
+	File aln_metrics_summary
+	File is_metrics_summary
 	File hap
-	File? fastqc
-	File? fastqscreen
+	File fastqc
+	File fastqscreen
 
 
 	String project
@@ -15,11 +15,7 @@ task extract_tables {
 	String disk_size
 
 	command <<<
-		if [ ${fastqc} ];then
-			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}
-		else
-			python /opt/extract_tables.py -hap ${hap} -project ${project}
-		fi
+		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}
 	>>>
 
 	runtime {
@@ -30,8 +26,8 @@ task extract_tables {
 	}
 
 	output {
-		File? pre_alignment = "pre_alignment.txt"
-		File? post_alignment = "post_alignment.txt"
+		File pre_alignment = "pre_alignment.txt"
+		File post_alignment = "post_alignment.txt"
 		File variant_calling = "variants.calling.qc.txt"
 	}
 }

tasks/extract_tables_vcf.wdl

@@ -0,0 +1,23 @@
+task extract_tables_vcf {
+
+	File hap
+	String project
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		python /opt/extract_tables.py -hap ${hap} -project ${project}
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File variant_calling = "variants.calling.qc.txt"
+	}
+}

tasks/multiqc_hap.wdl

@@ -0,0 +1,31 @@
+task multiqc_hap {
+
+	Array[File] summary
+
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		mkdir -p /cromwell_root/tmp/benchmark
+		cp ${sep=" " summary} /cromwell_root/tmp/benchmark
+		multiqc /cromwell_root/tmp/
+		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 hap = "multiqc_happy_data.json"
+	}
+}

workflow.wdl

@@ -8,8 +8,10 @@ import "./tasks/BQSR.wdl" as BQSR
 import "./tasks/Haplotyper.wdl" as Haplotyper
 import "./tasks/benchmark.wdl" as benchmark
 import "./tasks/multiqc.wdl" as multiqc
+import "./tasks/multiqc_hap.wdl" as multiqc_hap
 import "./tasks/merge_sentieon_metrics.wdl" as merge_sentieon_metrics
 import "./tasks/extract_tables.wdl" as extract_tables
+import "./tasks/extract_tables_vcf.wdl" as extract_tables_vcf
 import "./tasks/mendelian.wdl" as mendelian
 import "./tasks/merge_mendelian.wdl" as merge_mendelian
 import "./tasks/quartet_mendelian.wdl" as quartet_mendelian
@@ -19,7 +21,7 @@ import "./tasks/merge_family.wdl" as merge_family
 import "./tasks/filter_vcf.wdl" as filter_vcf
 
 
-workflow {{ project_name }} {
+workflow project_name {
 
 	File? fastq_1_D5
 	File? fastq_1_D6
@@ -711,7 +713,7 @@ workflow {{ project_name }} {
 			disk_size=disk_size	
 		}
 
-		call extract_tables.extract_tables as extract_tables_big {
+		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,
@@ -846,28 +848,17 @@ workflow {{ project_name }} {
 
 	    Array[File] benchmark_summary_hap = [benchmark_D5_vcf.summary, benchmark_D6_vcf.summary, benchmark_F7_vcf.summary, benchmark_M8_vcf.summary]
 
-		call multiqc.multiqc as multiqc_vcf {
+		call multiqc_hap.multiqc_hap as multiqc_hap {
 			input:
-			read1_zip="",
-			read2_zip="",
-			txt1="",
-			txt2="",
-			zip="",
 			summary=benchmark_summary_hap,
 			docker=MULTIQCdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size
 		}
 
-		call extract_tables.extract_tables as extract_tables_vcf {
+		call extract_tables_vcf.extract_tables_vcf as extract_tables_vcf {
 			input:
-			quality_yield_summary="",
-			wgs_metrics_summary="",
-			aln_metrics_summary="",
-			is_metrics_summary="",
-			fastqc="",
-			fastqscreen="",
-			hap=multiqc_vcf.hap,
+			hap=multiqc_hap.hap,
 			project=project,
 			docker=DIYdocker,
 			cluster_config=SMALLcluster_config,