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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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[DEV] Creating a Bash script to check logs #65

Closed Mxrcon closed 1 day ago

Mxrcon commented 2 years ago

Hey :wave:, Complementing our discussion on today's meeting, I decided to create a small bash script to check two things:

  1. Logs existence
  2. If the logs exist, look for errors

The script should be very simple and easily expansible so whenever we find new residual log files into MTBseq, we can easily add a config to check it!

I've tested the script with logfiles obtained from the latest parallel run, it'd be nice if you could test the bash script with other logs!

This Pull Request closes #63

Feel free to add your thoughts! I'm available to do any requested change!

Kindly, Davi!

abhi18av commented 2 years ago

Thank you for the initiative here @Mxrcon!

I'd like to evaluate this on my end as well and till that time, I request you to stick to the latest release v0.9.3 https://github.com/mtb-bioinformatics/mtbseq-nf/tree/v0.9.3

abhi18av commented 1 day ago

Closing this PR since to actually merge this with the new version would require more work than just simply restarting it.

I do want to thank @Mxrcon for his good work, maybe we can visit this again after the publication.

Mxrcon commented 19 hours ago

I agreed @abhi18av, But I'd like to add this PR as a register of why we decided to add | true to all processes using MTBseq. Debugging log files allowed us to understand the odd exit codes and why using true allowed us to successfully implement the pipeline.