feat: explicitly specify bwa index in bwa wrappers #232
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I really like the new behaviour and the backwards compatibility. I have some suggestions to update the example rules in the Snakefiles accordingly. But I also just realised, that PR #186 also addresses this. Could you double check whether you can contribute anything to the review over there? And if that PR addresses everything you're looking for, maybe close this PR here?
The changes regarding wrapper code rendering should be fine, as they are already in master in exactly the same way. No clue, why they get highlighted again.
| elif "index" in snakemake.input.keys(): | ||
| index = path.splitext(snakemake.input["index"])[0] |
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I guess this is intended as the standard future use, right? I would then update the example rule in the Snakefile to contain an input: index="someindex.some_index_extension" accordingly.
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Actually the input should list all index files, by making use of the multiext helper.
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You are right, miltiext is now displayed in the snakefiles.
…akemake-wrappers into bwa_index_auto_prefix
test logs are not available any more
…dled automatically by snakemake
johanneskoester
changed the title
Hi,
This is an implementation of enhancement request #228
Many thanks in advance for your reviews
PS: I'm still having this Template merge from PR #187 . I shall not have merged it to my master branch