Change flatfile-to-json.cwl to add_NCBI_annotation_track.cwl

[mpoelchau]

Related to #66.

It would be great if we could change the current flatfile-to-json.cwl to a workflow that runs add_NCBI_annotation_track.py, instead:

https://github.com/NAL-i5K/ColorByType/blob/master/scripts/add_NCBI_annotation_track.py

Parameters needed:

• -path /app/data/WebApollo_deployment/apollo_master/jbrowse/bin/flatfile-to-json.pl (we might want to deprecate this in the future, but for now let's add it in)
• -gff <path-to-gff>
• -out <path-to-jbrowse-data-directory>
• -organism <genus_species> (underscore _ between genus and species is important)
• -trackLabel1 <gggsss_current_models>
• -release <release-number> ( might need a new entry in the yml file for this...)
• -source <url-to-genomic-gff>

Example command:
add_NCBI_annotation_track.py -path /app/data/WebApollo_deployment/apollo_master/jbrowse/bin/flatfile-to-json.pl -gff /app/data/working_files/galmel/ASM364042v2/scaffold/analyses/Galleria_mellonella_Annotation_Release_101/galmel_final_for_apollo.gff -out /app/data/other_species/galmel/ASM364042v2/jbrowse/data -organism Galleria_mellonella -trackLabel1 galmel_current_models -release 101 -source ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/640/425/GCF_003640425.2_ASM364042v2/GCF_003640425.2_ASM364042v2_genomic.gff.gz

[mpoelchau]

Done, see https://github.com/NAL-i5K/Organism_Onboarding/blob/master/flow_apollo2_data_processing/processing/flatfile-to-json.cwl