Option to save cluster representative

[apcamargo]

An option to save cluster representatives to an output directory would simplify most dereplication pipelines. Currently, if the user wants to get the FASTA files of the dereplicated genomes it need to first parse galah's output and then move/copy the representative genomes to the desired location.

[apcamargo]

Thanks!

[wwood]

Hi,

I've added an option --output-representative-fasta-directory for this (which makes symlinks to absolute paths) and also --output-representative-list for just a list of the reps. I'm not 100% convinced about symlinking rather than copying, just trying to be nice to all the sysadmins out there.

Also now there is no stdout by default - an output mode must be chosen.

Let me know if there's anything else.

[apcamargo]

As a user, I'd feel safer if the files were copied. A typical pipeline for a disk-constrained environment would be:

Bin each sample -> Dereplicate bins from all samples and save them to a directory -> Delete invidivual-sample bins

[wwood]

Hi,

I've added that functionality with by adding --output-representative-fasta-directory-copy now. Thanks again for the suggestion.

[apcamargo]

Thanks Ben!