revised-bedtools-task

input_samples_file.tsv

-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	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	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
+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
+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

inputs

   "{{ 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",
-  "{{ project_name }}.bedtools.disk_size": "{{disk_size}}",
-  "{{ project_name }}.cp_bam.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
-  "{{ project_name }}.cp_bam.disk_size": "{{disk_size}}"
+  "{{ project_name }}.bedtools.disk_size": "{{disk_size}}"
 }

tasks/bedtools.wdl

 task bedtools {
 
-	Array[File] tmp_bam
+	Array[File] input_samples
 	File bed_file
 
 	String docker
 
 	command <<<
 	    set -e -o pipefail
-		cat ~{sep=" " tmp_bam}|bedtools multicov -bed ${bed_file} > revread_count.txt 
+		cat ~{sep=" " input_samples}|bedtools multicov -bed ${bed_file} > revread_count.txt 
 
 	>>>
 

tasks/cp_bam.wdl

-task cp_bam {
-
-	File bam
-    String bamname = basename(bam,".bam")
-
-	String cluster_config
-	String disk_size
-
-	command <<<
-	    set -e -o pipefail
-		cp ${bam} ${bamname}_tmp.bam
-	>>>
-
-	runtime {
-		cluster:cluster_config
-		systemDisk:"cloud_ssd 40"
-		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File tmp_bam = "${bamname}_tmp.bam"
-	}
-}

workflow.wdl

-import "./tasks/cp_bam.wdl" as cp_bam
 import "./tasks/bedtools.wdl" as bedtools
 
 workflow {{ project_name }} {
 	File input_samples_file
 	File bed_file
 	Array[Array[File]] input_samples = read_tsv(input_samples_file)
-    
-	scatter (sample in input_samples) {
-		call cp_bam.cp_bam as cp_bam {
-			input:
-			bam=sample[0]
-		}
-	}
 
 	call bedtools.bedtools as bedtools {
 			input:
-			tmp_bam=cp_bam.tmp_bam,
+			input_samples=input_samples,
 			bed_file=bed_file
-			
+
 	}
 }