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fix: bug with -O being used for gap opening penalty and samtools output directory #6

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fix: bug with -O being used for gap opening penalty and samtools output directory #6

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3cfaa10
add gap_penalty to params
huzuner Jun 20, 2023
7ff777b
[skip ci]
korbit-ai[bot] Aug 29, 2024
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2 changes: 2 additions & 0 deletions bio/minimap2/aligner/wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
sort = snakemake.params.get("sorting", "none")
sort_extra = snakemake.params.get("sort_extra", "")
gap_opening = snakemake.params.get("gap_opening", "")
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category Error Handling

The code retrieves the 'gap_opening' parameter from snakemake using snakemake.params.get("gap_opening", ""). However, if this parameter is not provided in the snakemake configuration, it will default to an empty string. This can lead to invalid command line arguments being passed to minimap2 if the empty string is used as the value for the '-O' option.

To handle this case more robustly, consider providing a default value for the 'gap_opening' parameter. For example, you can modify the line to: gap_opening = snakemake.params.get("gap_opening", "0"). This way, if the parameter is not specified, it will default to "0" instead of an empty string, ensuring a valid value is always passed to minimap2.

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out_ext = infer_out_format(snakemake.output[0])

Expand Down Expand Up @@ -45,6 +46,7 @@
"(minimap2"
" -t {snakemake.threads}"
" {extra} "
" -O {gap_opening} "
" {snakemake.input.target}"
" {snakemake.input.query}"
" {pipe_cmd}"
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