Fixed genome only option not working

[FernandoDuarteF]

Fixed --genome_only option not working.

[chriswyatt1]

Great, ok, lets wait for our first review, and then push it. I will test it now

[FernandoDuarteF]

As mentioned in #53:

• Fixed uncompressing on fasta and gff files not working, as done in decontamination workflow #72.
• Improved readability by being more explicit about what each item is in mapping functions.
• Fixed sync problems:
  • Changed CREATE_PATH so it now outputs a single tuple.
  • Combined fasta and gff channels into a single channel and then splitted then into different two channels using multiMap operator. Same thing for NCBIGENOMEDOWNLOAD input.

[FernandoDuarteF]

Hi @chriswyatt1, looks like meryl and merqury are working fine on the test datasets.

I think this is ready to be merged.

[chriswyatt1]

That all looks good, have tested it and works as expected. Questions/Comments:

1. Will the pipeline now work with mixed inputs, e.g. some with just genomes, other with refseq IDs, etc.?

2. Maybe we should add a option on the REAMDE for this already.
   Although the README does require a revamp with all the new modules/subworkflows added.

[FernandoDuarteF]

1. Will the pipeline now work with mixed inputs, e.g. some with just genomes, other with refseq IDs, etc.?

It works like this:

• If --genome_only is set, it will run on GENOME_ONLY mode, it will check if there is a genome present and run. Doesn't check for annotation. If you provide it, it will ignore it.
• If no --genome_only is set, it will run on GENOME_AND_ANNOTAION mode. It will check for RefSeq ID or local fasta and gff. If not present, it will fail.
  Note to myself: I need to improve the error messages.

2. Maybe we should add a option on the REAMDE for this already.
   Although the README does require a revamp with all the new modules/subworkflows added.

Yeah, I haven't look at the README. I'll check tomorrow and see what can I add. Probably a lot.

[FernandoDuarteF]

I also added .pre-commit-config.yaml to the repository which is needed to commit changes in gitpod.