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fix: Correctly handle non str index list for bwa-mem2/mem #4

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fix: Correctly handle non str index list for bwa-mem2/mem #4

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5644719
Correctly handle non str index list
Aug 6, 2024
3ef9dca
[skip ci]
korbit-ai[bot] Aug 21, 2024
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8 changes: 4 additions & 4 deletions bio/bwa-mem2/mem/wrapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,11 @@
bwa_threads = snakemake.threads
samtools_threads = snakemake.threads - 1

index = snakemake.input.get("index", "")
if isinstance(index, str):
index = path.splitext(snakemake.input.idx)[0]
idx = snakemake.input.get("idx", "")
if isinstance(idx, str):
index = path.splitext(idx)[0]
else:
index = path.splitext(snakemake.input.idx[0])[0]
index = path.splitext(idx[0])[0]
Comment on lines +30 to +34
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category Functionality

The changes you've made to use 'idx' instead of 'index' are good and address the reported issue. However, I suggest adding an explicit check for when 'idx' is not provided. Currently, if 'idx' is an empty string, it might lead to unexpected behavior. Consider adding a check like this:

idx = snakemake.input.get("idx", "")
if not idx:
    raise ValueError("No index file provided. Please specify 'idx' in the input.")

This will ensure that the wrapper fails early with a clear error message if the required index is not provided.

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# Check inputs/arguments.
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