We need to set up (yet another) workflow to process gene sets from NCBI's eukaryotic annotation pipeline for Chado import. This will be a standalone workflow (to happen after final_workflow.cwl, and before the 'setup production' workflow). We may eventually pipe all these together, but not for now.
I'm also willing to discuss whether this should be a cwl workflow at all at this point - since the scripts are still under development, perhaps cwl will be overkill at this point.
mpoelchau
commented
2 years ago
We need to set up (yet another) workflow to process gene sets from NCBI's eukaryotic annotation pipeline for Chado import. This will be a standalone workflow (to happen after final_workflow.cwl, and before the 'setup production' workflow). We may eventually pipe all these together, but not for now.
The workflow is currently a perl wrapper around some custom perl scripts. We can discuss re-writing these perl scripts as python, but since they are still in development I think perl is still preferred. https://gitlab.com/i5k_Workspace/monicas-data-processing-scripts/blob/master/process_NCBI_RefSeq_annotations_for_chado_ingest.pl
I'm also willing to discuss whether this should be a cwl workflow at all at this point - since the scripts are still under development, perhaps cwl will be overkill at this point.