revised-bedtools-task

input_samples_file.tsv

@@ -1,2 +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
+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

tasks/bedtools.wdl

@@ -9,7 +9,7 @@ task bedtools {
 
 	command <<<
 	    set -e -o pipefail
-		cat {sep=" " input_samples}|bedtools multicov -bed ${bed_file} > revread_count.txt 
+		cat ${sep=" " input_samples}|bedtools multicov -bed ${bed_file} > revread_count.txt 
 
 	>>>