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bwa-mem2 incorrect index #522
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@dlaehnemann @johanneskoester @tdayris |
I slept on it and realised that I'm going to modify the wrapper for cram output anyway. Since samtools sort needs the reference, input.ref makes sense. I am still against the "allow only one of the index files". |
I agree, all input files needed by the rule should be explicitely specified. |
Absolutely agreed, that all necessary input files should be required. That was even part of the original PR that got this snippet in there, but that buggy snippet slipped through review, sorry. The only part that was adjusted to require all index files was the example Snakefile... |
This issue was marked as stale because it has been open for 6 months with no activity. |
Bump to remove stale label. |
The wrapper 1.7.0 for bwa-mem2 contains the following code:
which mixes
index
andidx
, clearly a bug.PS: The command uses
samtools sort
, which would benefit from offering a temp directory.The text was updated successfully, but these errors were encountered: