bwa-mem2 "{tmp}.0000.bam": File exists about grenepipe HOT 5 CLOSED

Tried and the issue is resolved. Thanks!

from grenepipe.

Hi @RvV1979,

sorry you ran into this - that particular bug had been solved in the meantime after release v0.10.0, but I did not create a new release since. I have now, see grenepipe v0.11.0, which fixes this. You will have to edit the first data section of your config.yaml a little bit to work with the new release, and maybe some more sections - see its config file for the expected format.

Cheers
Lucas

from grenepipe.

Hi Lucas,
Thanks for the quick reply and for creating a new release based on the latest changes. However, I changed to grenepipe v0.11.0 and the issue remains*. Any advice or assistance would be greatly appreciated.

*FYI that the pipeline writes files named {tmp}.0000.bam etc in the main working directory, even though https://github.com/moiexpositoalonsolab/grenepipe/blob/master/scripts/bwa-mem2-mem.py seems to aim for the creation of a temporary directory:

# When using samtools, we create a temp dir.
if sort == "samtools":
    with tempfile.TemporaryDirectory() as tmp:
        shell( shell_cmd )
else:
    shell( shell_cmd )

Note also that I have not specified a temp directory in the main config.yaml (i.e., temp-dir: "")

from grenepipe.

Oh I see, that was indeed a subtle bug in the way that the particular script you pointed out uses the {tmp} variable... Fixed now on the master branch. Could you please try with that (the green Code button here, and then Download ZIP), and see if that works?

Thanks,
Lucas

from grenepipe.

Awesome! Release v0.11.1 contains the fix now.

from grenepipe.