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fix: typo on samtools regions file #43

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Merged
merged 2 commits into from
Mar 21, 2025
Merged

fix: typo on samtools regions file #43

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4a41162
Fix typo
fgvieira Mar 21, 2025
bcce33a
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fgvieira Mar 21, 2025
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11 changes: 5 additions & 6 deletions snakemake_wrapper_utils/samtools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,10 +31,9 @@ def get_samtools_opts(
sys.exit(
"You have specified number of threads (`-@/--threads`) in `params.extra`; this is automatically infered from `threads`."
)
samtools_opts += (
""
if snakemake.threads <= 1
else " --threads {}".format(snakemake.threads - 1)

if snakemake.threads > 1:
samtools_opts += f" --threads {snakemake.threads - 1}"
)

######################
Expand All @@ -55,11 +54,11 @@ def get_samtools_opts(
if parse_regions:
if is_arg("--region-file", extra) or is_arg("--regions-file", extra):
sys.exit(
"You have specified regions file (`--regions-file`) in `params.extra`; this is automatically infered from `regions` input file."
"You have specified regions file (`--region[s]-file`) in `params.extra`; this is automatically infered from `regions` input file."
)

if snakemake.input.get("regions"):
samtools_opts += f" --regions-file {snakemake.input.regions}"
samtools_opts += f" --region-file {snakemake.input.regions}"

###################
### Write index ###
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