Please provide a version cli flag to get package version

[luiskuhn]

Hi,

would it be possible to include a version flag in the mcmicro CLI ? (https://github.com/labsyspharm/scimap/blob/6880d225a10fd34da5150241e3a2b24c49df9bd7/scimap/cli/_scimap_mcmicro.py#L1)

Thanks

[jmuhlich]

Can you explain more about your use case? Do you want to be able to run scimap-mcmicro --version and have it print out the current version? Are you using scimap through mcmicro and you want to see the version used for a run? If it's the latter, this is already available in qc/params.yml inside each run.

[FloWuenne]

Just saw this issue from @luiskuhn and want to chime in to give context. For the nf-core implementation of the tools, nf-core catches the version number within the process by usually having the tool print the version number. We can manually provide it via a variable, but this means updating that variable for each new version number. The usage that you describe @jmuhlich scimap-mcmicro --version would be the one we would like to have for the nf-core module. Of course, we can also think about a more general nf-core module for SCIMAP in the future, but for now, the MCMICRO parser seemed the easiest and most fitting: https://nf-co.re/modules/scimap_mcmicro