output file name

[Phlya]

output file name

[Phlya]

Nice, sounds good. Just important for it to handle absolute and relative paths. Thank you!

[cmdoret]

Hi, this has been addressed in #28, I'll make a release soon when checks have passed :)

[cmdoret]

Hi @Phlya ,

Yes, I could add like a --prefix option. In a snakemake workflow, the output filenames would currently be:

output:
    tbl = "{sample}/loops_out.txt",
    win = "{sample}/loops_out.json"

whereas with a --prefix option, it would become:

output:
    tbl = "{sample}.txt",
    win = "{sample}.json"

Do you think the latter option would be more convenient to work with ?
In that case the command
chromosight detect sample.cool sample/
would become
chromosight detect --prefix sample sample.cool

I agree the possibility to customize output filenames would be nice. I'm just a bit concerned the CLI is becoming bloated with all the options. What do you think about a --prefix option ?

[Phlya]

Prefix is good! Assuming it allows to include a path to a different folder, and it's not just saved in the same folder with the prefix...

[cmdoret]

Right, it would be confusing to add --prefix while keeping a positional argument for the output directory, I think I'll simply replace the output directory argument by output prefix and remove predefined output filenames. This way, chromosight detect input.cool out_dir/output would produce out_dir/output.txt and out_dir/output.json. That seems more intuitive.

Thanks for the feedback, I'll get back to you. !

[cmdoret]

This is now the default behaviour in chromosight 1.2.0, thanks !

[Phlya]

Awesome, thanks!

[Phlya]

Very quick fix!