Update integrated_annotation.wdl

broadinstitute · Aug 18, 2023 · 3ffa949 · 3ffa949
1 parent 420b42c
commit 3ffa949
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/AnnotateBed/integrated_annotation.wdl b/AnnotateBed/integrated_annotation.wdl
@@ -153,10 +153,10 @@ task samtools_coverage {
        Int disk_size
     }
     command <<<
-        sed 's/^chr//' ~{bam_file} > rm_chr_tmp.bed
-        for region in `awk '{print $1":"$2"-"$3}' rm_chr_tmp.bed`
+        sed 's/^chr//' ~{bed_to_annotate} > rm_chr_tmp.bed
+        for region in `awk '{print $1":"$2"-"$3}' ${rm_chr_tmp.bed}`
         do
-           samtools coverage rm_chr_tmp.bed -r ${region} >> tmp
+           samtools coverage ~{bam_file} -r ${region} >> tmp
         done
         awk '/startpos/&&c++>0 {next} 1' tmp > ~{sample_id}.coverage.txt
 >>>