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Ensure genes of interest can be omitted
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This goes both for the bed file input (key is `bed`) and the list of
gene names, `genes_of_interest`.
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Redmar-van-den-Berg committed Nov 7, 2024
1 parent 4f02110 commit 4b7ec31
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Showing 2 changed files with 18 additions and 1 deletion.
1 change: 0 additions & 1 deletion includes/expression/scripts/coverage.py
Original file line number Diff line number Diff line change
Expand Up @@ -182,7 +182,6 @@ def main(
raw: bool,
) -> None:
if not bedfile and not genes:
print("Nothing to do")
exit(0)

coverage: dict[str, Coverage] = dict()
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18 changes: 18 additions & 0 deletions test/test_expression.yml
Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,24 @@
contains:
- "MT-CO2\t1.0\t1.0\t1.0"

# The output files will be empty, but it should not crash
- name: Test running the expression module without genes of interest or bed
tags:
- functional
- expression
- current
command: >
snakemake
--snakefile includes/expression/Snakefile
--workflow-profile test
--configfile test/data/config/expression.json
--config
pepfile=test/pep/expression.csv
exit_code: 0
files:
- path: SRR8615409/expression/coverage.csv
- path: SRR8615409/expression/coverage.normalized.csv

- name: Check formatting of Snakemake files
tags:
- sanity
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