@@ -9,7 +9,7 @@ task Dedup { | |||
command <<< | |||
set -o pipefail | |||
set -e | |||
/src/Bismark-0.20.1/deduplicate_bismark -p --bam ./$inputfile --output_dir ./ | |||
/src/Bismark-0.20.1/deduplicate_bismark -p --bam ${unsorted_bam} --output_dir ./ | |||
>>> | |||
runtime { | |||
docker:docker |