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bugfix for merge_and_reheader_bams WDL task #818

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merged 3 commits into from
Jun 7, 2018
Merged

bugfix for merge_and_reheader_bams WDL task #818

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3544868
forgot python subcommand
dpark01 May 29, 2018
1f5e06d
Merge branch 'master' into dp-merge-fix
tomkinsc May 31, 2018
e5a9ab0
Merge branch 'master' into dp-merge-fix
tomkinsc Jun 7, 2018
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2 changes: 1 addition & 1 deletion pipes/WDL/workflows/tasks/demux.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,7 @@ task merge_and_reheader_bams {
fi

if [ -f ${reheader_table} ]; then
read_utils.py merged.bam ${reheader_table} ${out_basename}.bam --loglevel DEBUG
read_utils.py reheader_bam merged.bam ${reheader_table} ${out_basename}.bam --loglevel DEBUG
else
echo "Skipping reheader, no mapping table specified"
ln -s merged.bam ${out_basename}.bam
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