search

MikkelSchubert / paleomix

Pipelines and tools for the processing of ancient and modern HTS data.
https://paleomix.readthedocs.io/en/stable/
MIT License
43 stars 19 forks source link

BWA backtrack additional options added to samse, not aln #49

Closed DeondeJager closed 1 year ago

DeondeJager commented 1 year ago

Hi Mikkel,

I added additional options (-n and -o) for bwa backtrack in the yaml file (bam pipeline), expecting them to be applied to the bwa aln command (as stated in the yaml file), but instead they seem to be applied to the bwa samse command (see log file), which then results in an error (I assume because bwa samse doesn't have a -o option). I've attached the yaml and log files, and I'm using paleomix v1.3.7. Please can you have a look to see what's going wrong here?

Cheers, Deon SCR_086_RmA009.yaml.txt bam_pipeline.20230515_151100_01.log

MikkelSchubert commented 1 year ago

Hi Deon,

Thank you for the report!

You are not doing anything wrong; that is a bug in paleomix. I'll release a fixed version Thursday or Friday.

Best, Mikkel

DeondeJager commented 1 year ago

Hi Mikkel,

OK, thanks for looking into it, and for pushing a fix soon - much appreciated!

Cheers, Deon

MikkelSchubert commented 1 year ago

I've released a version of paleomix that fixes this (v1.3.8). Thanks for the report and let me know if you run into any other problems.

Cheers, Mikkel