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NBISweden / GAAS

Genome Assembly and Annotation Service code
GNU General Public License v3.0
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Gaas create annotation project #82

Closed nylander closed 2 years ago

nylander commented 2 years ago

This is a new version of the script gaas_create_annotation_project.pl as per request from @LucileSol.

Now it basically creates a folder hierarchy, and does not require mandatory arguments (for copying genome.fas etc).

NOTE: The previous script had an option -v which was used for supplying the assembly version. This is now changed!

If one want to supply assembly version, the new option is --assembly-version (or -a).

The option -v (or --version) is now used for printing the version of the script itself.

This change in options can of course be undone.

LucileSol commented 2 years ago

seems all good to me! @aersoares81 want to try it? or add something?

aersoares81 commented 2 years ago

Looks good, I'll give it a try soon-ish. I have a couple of suggestions of things we could add to it, we'll talk on Wednesday. :)

aersoares81 commented 2 years ago

Some suggestions after out meeting today:

1) Add an additional directory "public_data" where we can store stuff for Maker's Protein Homology Evidence; 2) An option to symlink or copy RNAseq data from somewhere else into the project folder; 3) AnnotationPreprocessing.nf that we use to pre-process/clean the genome assemblies will output the "purified" version of the genome to a directory called to 'assembly/${fasta_file.baseName}_purified'. The original genome is inside /Genome. I think having these two directories is a bit redundant, so we either create 'assembly' instead of 'Genome', or change the output of AnnotationPreprocessing.nf to inside Genome instead.