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/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/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

tasks/bedtools.wdl

 task bedtools {
 
-	Array[File] input_samples
+	Array[File] bam
+	Array[File] bai
 	File bed_file
 
 	String docker
 
 	command <<<
 	    set -e -o pipefail
-		bedtools multicov -bams ${sep=' ' input_samples} -bed ${bed_file} > revread_count.txt 
+		mkdir -p  /cromwell_root/tmp/bedtools
+		cp ${sep=' ' bai} /cromwell_root/tmp/bedtools
+		cd /cromwell_root/tmp/bedtools
+		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt 
 
 	>>>
 

workflow.wdl

 
 	File input_samples_file
 	File bed_file
-	Array[File] input_samples = read_lines(input_samples_file)
+	Array[Array[File]] input_samples = read_tsv(input_samples_file)
+	Array[File] bam = input_samples[0]
+	Array[File] bai = input_samples[1]
 	call bedtools.bedtools as bedtools {
 			input:
-			input_samples=input_samples,
+			bam=bam,
+			bai=bai,
 			bed_file=bed_file
 
 	}