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tasks/BAMReadCount.wdl
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| @@ -12,7 +12,7 @@ task BAMReadCount { | |||
| String disk_size | |||
| command <<< | |||
| bam-readcount -w 0 -q1 -f ${fa} -l ${bed} ${bam} > ${sample_id}.readcount | |||
| bam-readcount -w 0 -q1 -f ${ref_dir}/${fa} -l ${bed} ${bam} > ${sample_id}.readcount | |||
| >>> | |||
| runtime { | |||
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