fixup

inputs

@@ -5,6 +5,7 @@
   "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bismark:1.1.0_20190225",
   "{{ project_name }}.sample": "{{ sample_name }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}", 
-  "{{ project_name }}.fastq_2": "{{ read2 }}"
+  "{{ project_name }}.fastq_2": "{{ read2 }}",
+  "{{ project_name }}.chrom_sizes": "oss://choppy-app-example-data/WGBS/hg38.chrom.sizes"
 }
 

tasks/Call_meth.wdl

@@ -1,7 +1,7 @@
 task Call_meth {
 	
 	File ref_dir
-    
+	File chrom_sizes
 	File Dedup_bam
 	String sample
 	String docker
@@ -11,7 +11,10 @@ task Call_meth {
 command <<<
 		set -o pipefail
 		set -e
-		/src/Bismark-0.20.1/bismark_methylation_extractor --multicore 16 -p --no_overlap --comprehensive --report --bedGraph --cytosine_report --CX_context --ignore_r2 2 --merge_non_CpG --genome_folder ${ref_dir} ${Dedup_bam}
+		/src/Bismark-0.20.1/bismark_methylation_extractor --multicore 16 -p --no_overlap --comprehensive --report --bedGraph --cytosine_report -o ./ --gzip --ignore_r2 2 --genome_folder ${ref_dir} ${Dedup_bam}
+		gunzip "${sample}.deduplicated.bedGraph.gz"
+		bedtools sort -i ${sample}.deduplicated.bedGraph > ${sample}.deduplicated.sorted.bedGraph
+		/usr/local/bin/bedGraphToBigWig ${sample}.deduplicated.sorted.bedGraph ${chrom_sizes} ${sample}.deduplicated.bw
 	>>>
 	
 	runtime {
@@ -22,13 +25,14 @@ command <<<
 	}
 
 	output {
-		File bedGraph = "${sample}.deduplicated.bedGraph.gz"
-		File cov = "${sample}.bismark.deduplicated.cov.gz"
-		File splitting_report = "${sample}.deduplicated_splitting_report.txt"
-		File CHG_context = "CHG_context_${sample}.deduplicated.txt"
-		File CHH_context = "CHH_context_${sample}.deduplicated.txt"
-		File CpG_context = "CpG_context_${sample}.deduplicated.txt"
+		File BedGraph = "${sample}.deduplicated.bedGraph"
+		File Bigwig = "${sample}.deduplicated.bw"
+		File Cov = "${sample}.deduplicated.bismark.cov.gz"
+		File Splitting_report = "${sample}.deduplicated_splitting_report.txt"
+		File CHG_context = "CHG_context_${sample}.deduplicated.txt.gz"
+		File CHH_context = "CHH_context_${sample}.deduplicated.txt.gz"
+		File CpG_context = "CpG_context_${sample}.deduplicated.txt.gz"
 		File Mbias = "${sample}.deduplicated.M-bias.txt"
-		File CX = "${sample}.CX_report.txt"
+		File CX = "${sample}.CX_report.txt.gz"
 	}
-}
+}

workflow.wdl

@@ -9,6 +9,7 @@ workflow {{ project_name }} {
 	File fastq_1
 	File fastq_2
 
+	File chrom_sizes
 	String sample
 	String docker
 	
@@ -40,6 +41,7 @@ workflow {{ project_name }} {
 	call Call_meth.Call_meth as Call_meth {
 		input:
 		ref_dir=ref_dir,
+		chrom_sizes=chrom_sizes,
 		Dedup_bam=Dedup.Dedup_bam,
 		sample=sample,
 		docker=docker,