--mc option for runNanoSeq.py indel

[monagai]

In a recommended procedure in README, --mc 16 is set for runNanoSeq.py indel.
However, it causes an error runNanoSeq.py: error: unrecognized arguments: --mc 16.
Is the correct option for it -z?

P.S. extract-tags.py in README is a mistake for extract_tags.py.

[fa8sanger]

Sorry about that, the README needs a couple of updates, especially regarding the indel pipeline.
If you run runNanoSeq.py indel --help you will see that parameters have been changed:
optional arguments:
-h, --help show this help message and exit
-s SAMPLE, --sample SAMPLE
sample name in output vcf (sample_1)
--rb RB minimum reads in a bundle. (2)
--t3 T3 excess bases above this value are trimmed from 3'
(136)
--t5 T5 bases to trim from 5' reads (8)
-a A minimum AS-XS (50)
-c C fraction of clips (0.02)
-z Z minimum normal coverage (mc) (15)
-v V maximum normal VAF (0.01)

You are right -mc corresponds now to -z. We changed it to match the argument naming in the var command.
I hope this helps

[monagai]

I really thank you for your quick reply!