Non-absolute paths don't resolve about ultra HOT 5 CLOSED

Tested and validated 👍
Thanks for the patch!
The bioconda recipe has been updated.
The nf-core update is in process.

from ultra.

I implemented the change proposed above and I uploaded it as a new version of uLTRA to PyPI (v0.0.4.1 https://pypi.org/project/ultra-bioinformatics/). Let me know if this resolves the issue.

from ultra.

Super, thanks! I'll close this then.

from ultra.

Hi @lassefolkersen

After looking into this, I think it would suffice to change within uLTRA lines 61-69 to

    elif not args.disable_infer:
        db = gffutils.create_db(args.gtf, dbfn=database, force=True, keep_order=True, merge_strategy='merge', 
                                sort_attribute_values=True)
        db = gffutils.FeatureDB(database, keep_order=True)
    else:
        db = gffutils.create_db(args.gtf, dbfn=database, force=True, keep_order=True, merge_strategy='merge', 
                                sort_attribute_values=True, disable_infer_genes=True, disable_infer_transcripts=True)

That is, removing the unnecessary line fn = gffutils.example_filename(args.gtf).

This would solve the issue of requiring an absolute path within the program and it doesn't require any change in the call to the program.

Would this be good?

from ultra.

I think so - but the verdict really is if it can run the nf-core unit tests. Not whether I like it or not. I can help with running some tests if you'd like. (or just pull down the test-module yourself and maybe replace the containers line to something local where you have your changes in)

from ultra.