bwa-memx_index meme wrapper expects specific file name?

[Phlya]

From what I can tell, the wrapper bwa-memx/index in case of bwa=bwa-meme expects one of the output to be named exactly as {input[0]}.suffixarray_uint64. This file is produced by the first indexing step, and then this exact name is used by the second step. It's is clear from the code of the wrapper:

snakemake-wrappers/bio/bwa-memx/index/wrapper.py

Line 77 in a23858a

suffixarray = snakemake.input[0] + ".suffixarray_uint64"

Same thing in the bwa-meme wrapper btw:

snakemake-wrappers/bio/bwa-meme/index/wrapper.py

Line 48 in a23858a

suffixarray = snakemake.input[0] + ".suffixarray_uint64"

[github-actions]

This issue was marked as stale because it has been open for 6 months with no activity.

[fgvieira]

I am not familiar with bwa-meme but, from what I understand, bwa-meme index creates several files. One of them is snakemake.input[0] + ".suffixarray_uint64", that is needed as input for bwa-meme-train-prmi, no?

[Phlya]

From what I remember (it's been a while), the problem is with the case when I have run index manually with a different prefix, and want to rely on snakemake not rerunning jobs for which the output exists. So I can't specify the output files, if they are named different than snakemake expects... (and the suffixes have to be exactly the same for the mapping to work, but the prefix can be anything...)