The cstmm help message is not accurately described

[kfuku52]

@Hego-CCTB Could you improve this? --ortho actually requires a subdirectory of OrthoFinder outdir. The description of --count is also unclear; It should be explicitly mentioned that this option expect amalgkit merge outputs. If appropriate, --count may be renamed to standardize the options among amalgkit subcommands.

usage: amalgkit cstmm [-h] [-w PATH] --ortho PATH --count PATH

optional arguments:
  -h, --help            show this help message and exit
  -w PATH, --out_dir PATH
                        default=./: output directory.
  --ortho PATH          default=./: OrthoFinder results directory.
  --count PATH          default=./: Folder path to where count data is stored.

[Hego-CCTB]

sure, no problem!

[Hego-CCTB]

I made slight changes. I can be more specific, but I'd like to keep these short and refer to the wiki for more detailed usage.

  -w PATH, --out_dir PATH
                        default=./: output directory.
  --ortho PATH          default=./: Path to "Orthogroups" folder from
                        OrthoFinder Results output.
  --count PATH          default=./: Folder path to count data as produced by
                        `amalgkit merge`. Run `amalgkit merge` after `amalgkit quant`.

[kfuku52]

OK!