fix

inputs

@@ -6,6 +6,8 @@
   "{{ project_name }}.sample": "{{ sample_name }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}", 
   "{{ project_name }}.fastq_2": "{{ read2 }}",
-  "{{ project_name }}.chrom_sizes": "oss://choppy-app-example-data/WGBS/hg38.chrom.sizes"
+  "{{ project_name }}.chrom_sizes_dir": "oss://choppy-app-example-data/WGBS/chrom_sizes/",
+  "{{ project_name }}.chrom_sizes": "hg38.chrom.sizes"
+  
 }
 

tasks/Call_meth.wdl

@@ -1,8 +1,9 @@
 task Call_meth {
 	
 	File ref_dir
-	File chrom_sizes
+	File chrom_sizes_dir
 	File Dedup_bam
+	String chrom_sizes
 	String sample
 	String docker
 	String cluster_config
@@ -14,7 +15,7 @@ command <<<
 		/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
+		/usr/local/bin/bedGraphToBigWig ${sample}.deduplicated.sorted.bedGraph ${chrom_sizes_dir}/${chrom_sizes} ${sample}.deduplicated.bw
 	>>>
 	
 	runtime {

workflow.wdl

@@ -9,10 +9,10 @@ workflow {{ project_name }} {
 	File fastq_1
 	File fastq_2
 
-	File chrom_sizes
+	File chrom_sizes_dir
 	String sample
 	String docker
-	
+	String chrom_sizes
 
 	String disk_size
 	String cluster_config
@@ -41,6 +41,7 @@ workflow {{ project_name }} {
 	call Call_meth.Call_meth as Call_meth {
 		input:
 		ref_dir=ref_dir,
+		chrom_sizes_dir=chrom_sizes_dir,
 		chrom_sizes=chrom_sizes,
 		Dedup_bam=Dedup.Dedup_bam,
 		sample=sample,