Documentation update

[susheelbhanu]

Hi all,

I'm running eukulele using the latest version available on conda and getting the following error:

usage: eukulele [subroutine] --mets_or_mags [dataset_type] --sample_dir [sample_directory] --reference_dir [reference_database_location] [all other options]
EUKulele: error: argument subroutine: invalid choice: '/hdd0/susbus/results/eukulele_input' (choose from '', 'all', 'download', 'setup', 'alignment', 'busco', 'coregenes')
Running EUKulele with command line arguments, as no valid configuration file was provided.

The current documentation does not reflect the need to input the subroutine flag. Could you please update this when possible?

Thank you!

[akrinos]

Hello @susheelbhanu ! What's going on here is that it appears that you have added the input directory and the program is not recognizing that it's a flag argument - could you paste the full command you're using? The error suggests that the path is being interpreted as a subroutine not because a subroutine was required but rather because no flag was included before this argument (so it figures you intended it to be a subroutine).

[susheelbhanu]

@akrinos thanks for the quick response. The error seems to be fixed now, but just for legacy sake, here is how I have it setup: EUKulele all -m mets --sample_dir {input} --out_dir {output[0]} --database {params.db} --scratch {params.scratch} --CPUs {threads} --alignment_choice {params.aligner} --reference_dir {params.ref_dir}

Thank again!