Aviti index fixer

[ssjunnebo]

A new index fixer script for Aviti run manifest.
Usage:

Usage: aviti_index_fixer.py [OPTIONS]

  Main function to fix the samplesheet indexes for AVITI runs.

Options:
  --manifest_path TEXT  Path to the sample manifest. e.g. ~/fc/AVITI_run_manif
                        est_2450545934_24-1214961_250722_154957_EunkyoungChoi_
                        untrimmed.csv  [required]
  --project TEXT        Project ID, e.g. P10001. Only the indexes of samples
                        with this specific project ID will be changed. Use
                        multiple times for multiple projects.
  --swap                Swaps index 1 and 2.
  --rc1                 Exchanges index 1 for its reverse compliment.
  --rc2                 Exchanges index 2 for its reverse compliment.
  --add_sample TEXT     Include additional sample(s). Use multiple times for
                        multiple samples, or provide a file. Each new sample
                        should have the same format as in the existing
                        manifest. Example: --add_sample P12345,ATCG,CGTA,1,A__
                        Project_25_16,301-10-10-301,ATCG-CGTA,
  --help                Show this message and exit.

[aanil]

👍

[FranBonath]

Looks great! I have a few minor questions and one suggestion that may help: Could we make the printed text after an action the exact text we could use in a FC running note? Then we only would need to copy paste that...

It's not super important, but I think it would save a little bit of time.