Open vsoch opened 4 years ago
We will fix this with an additional test in snakemake itself. The freedom to specify a prefix might be important for some scenarios, so I'd rather not like to remove it.
However, keeping this open until we have a proper test for this in the snakemake github action.
Snakemake version 5.10.0
Describe the bug For each of bwa index and bwa mem the user might put in a prefix that will work for a local job, but fail given a remote. Examples are provided below:
Bwa Mem
For bwa mem, note that the params has an "index" below that is used to specify the path. The first below I don't think will work:
But this would:
Unlike bwa index (discussed next) I'm not sure we can just remove this one.
Bwa Index
For this prefix, given running on a remote with this recipe:
The error log will report that bwa/genome.pac cannot be found. It's not the inputs or outputs, but rather that prefix is used to determine the path to the file! The correct usage would be:
But rather we aren't required to specify it, so even better would be to remove it entirely:
Of course the user writing the pipeline might not know this, in which case maybe there should be a fix to allow for a prefix specified that would, given a default remote prefix, add it as well?
For both of the above, if I can get started on work to fix the wrappers and then do a PR here, I'd be happy to do that! I'm not sure if there are other cases like this too in the wrappers. Let me know your thoughts.