generate readme files for assemblies and gene predictions

[mpoelchau]

This issue contains guidelines on how to auto-generate readme files (see parent issue #87)

• The idea is to take the 2 readme templates below, and auto-fill as much as we can in the square brackets [].
  • assembly template: https://gitlab.com/i5k_Workspace/organism-setup-templates/-/blob/master/scaffold_readme_template
  • gene prediction template: https://gitlab.com/i5k_Workspace/organism-setup-templates/-/blob/master/annotations_readme_template
• Outputs are the filled-in readme files.
  • assembly readme - final file name should be readme.txt, should end up in the scaffold directory
  • gene prediction readme - final file name should be readme.txt, should end up in the annotations sub-directory (I think that's $(inputs.tree[2]))
• This new workflow should be included in final-workflow.cwl. The order in final-workflow.cwl should probably be before flow_dispatch, and the files will probably need to be moved in the flow_dispatch workflow.
• Right now the templates are in a separate gitlab repo. We don't have to keep them there, though - if it's easier to just include the full text in the cwl file, let's do that

Gene prediction template instructions:

• [optional: Organization] - add an entry to yml file, default value:NCBI
• [date-downloaded-or-received] - can this be auto-generated by cwl, based on the date that the pipeline is run? If not, add an entry to yml file, default value: 2020-30-01
• [URLs-to-genome-files] - These are the URLS to the genome gff, and all fastas.
• [link-to-i5kworkspace-analysis-page] - i think this can be https://i5k.nal.usda.gov/content/ncbi-$(inputs.tree[2]) (e.g. https://i5k.nal.usda.gov/content/ncbi-galleria-mellonella-annotation-release-101)
• [link-to-publication-if-available] - add an entry to yml file, default value: Not published, please follow Ft. Lauderdale/Toronto guidelines for data reuse
• [describe post-processing, if any] - leave in brackets, data wrangler will update manually
• [Filename] - leave in brackets, data wrangler will update manually

Assembly template instructions:

• [optional: Organization] - add an entry to yml file, default value:NCBI
• [date-downloaded-or-received] - can this be auto-generated by cwl, based on the date that the pipeline is run? If not, add an entry to yml file, default value: 2020-30-01
• [URLs-to-genome-files] - this is the URL to the genome fasta.
• [link-to-i5kworkspace-analysis-page] -
  • i think this can be https://i5k.nal.usda.gov/content/$genus-$species-genome-assembly-$(inputs.tree[1])-$(inputs.accession) (e.g. https://i5k.nal.usda.gov/content/galleria-mellonella-genome-assembly-asm364042v2-gcf0036404252)
  • and that means we'd need a new input parameter in the yml file, default value:GCF0036404252
• [link-to-publication-if-available] - add an entry to yml file, default value: Not published, please follow Ft. Lauderdale/Toronto guidelines for data reuse
• [file] - leave in brackets, data wrangler will update manually
• [describe post-processing, if any]- leave in brackets, data wrangler will update manually
• [Filename] - leave in brackets, data wrangler will update manually

[mpoelchau]

Completed via #94.