revised-bedtools-task

input_bai.tsv

@@ -0,0 +1,2 @@
+oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/43061775-40e6-47e7-8f07-b961b44c596f/call-samtools/GCCACATA_S9_L001_R1_001.sorted.bam.bai
+oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/49bd025e-5275-4fbd-9e67-b279b08ce8b5/call-samtools/F1_S6_L001_R1_001.sorted.bam.bai

inputs

@@ -1,5 +1,6 @@
 {
-  "{{ project_name }}.input_samples_file": "{{ input_samples_file }}",
+  "{{ project_name }}.input_bam_file": "{{ input_bam_file }}",
+  "{{ project_name }}.input_bai_file": "{{ input_bai_file }}",
   "{{ project_name }}.bed_file": "oss://pgx-reference-data/reference/bedtools/ERVmap_v2_all_sorted.bed", 
   "{{ project_name }}.bedtools.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
   "{{ project_name }}.bedtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",

tasks/bedtools.wdl

@@ -1,6 +1,7 @@
 task bedtools {
 
 	Array[File] bam
+	Array[File] bai
 	File bed_file
 
 	String docker
@@ -9,7 +10,9 @@ task bedtools {
 
 	command <<<
 	    set -e -o pipefail
-		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt 
+        path=$(dirname ${sep=' ' bam})
+        mv ${sep=' ' bai} $path
+		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt
 
 	>>>
 

workflow.wdl

@@ -2,14 +2,16 @@ import "./tasks/bedtools.wdl" as bedtools
 
 workflow {{ project_name }} {
 
-	File input_samples_file
+	File input_bam_file
+	File input_bai_file
 	File bed_file
-	Array[File] bam = read_lines(input_samples_file)
+	Array[File] bam = read_lines(input_bam_file)
+	Array[File] bai = read_lines(input_bai_file)
 	call bedtools.bedtools as bedtools {
 			input:
 			bam=bam,
+			bam=bai,
 			bed_file=bed_file
-
 	}
 }