support simplified samples.csv / prefix usage #11
Comments
bluegenes
added a commit
to sourmash-bio/sourmash_plugin_branchwater
that referenced
this issue
Mar 1, 2024
## Prefix-based sketching #184 introduces a new input type that better supports metagenome reads, but doesn't really make things that much simpler for the power user. We can probably support prefix-style naming, as suggested in dib-lab/sourmash-slainte#11. Here we introduce a 'prefix' CSV type with the following columns: `name,input_moltype,prefix,exclude`. Here we: 1. glob to find all files that match prefix 2. glob to find all files that match exclude 3. filter prefix files to exclude `exclude` files This just uses `glob`, no `regex`, so `*` are fine in `prefix` and `exclude`, but not full regex patterns.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
in practice a lot of samples stuff seems to be "use this prefix, find paired end files, sketch".
could just write a script or set of scripts to generate samples.csv for different situations, actually...
so an alternative could be: samples.csv gets more complicated, but is easier to autogenerate?
The text was updated successfully, but these errors were encountered: