Skip to content

Commit

Permalink
Refactor pileup_norm.smk to remove extendReads and -e options for unp…
Browse files Browse the repository at this point in the history
…aired samples
  • Loading branch information
alsmith151 committed Apr 21, 2024
1 parent 7c28520 commit 22060e1
Showing 1 changed file with 4 additions and 0 deletions.
4 changes: 4 additions & 0 deletions seqnado/workflow/rules/pileup_norm.smk
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,10 @@ def format_deeptools_bamcoverage_options(wildcards):

if "--scaleFactor" in options:
options = re.sub("--scaleFactor [0-9.]+", "", options)

if not DESIGN.query(wildcards.sample).is_paired:
options = re.sub(r"--extendReads", "", options)
options = re.sub(r"-e", "", options)

return options

Expand Down

0 comments on commit 22060e1

Please sign in to comment.