Added the logic to use genus level alignments #478
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I'm thinking we might need some clade-level decision making for whether to use genus level data or not. What clade(s) has this been tested on so far?
I'd also like to understand where @ens-ftricomi investigation of the long-read consensus code got to, and how we could merge that here?
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PR details
Is this a fix/ update/ new feature?
new_feature
Include a short description
I have added a logic in the long read pipeline to use the genus level alignments when the species level is absent. It is worth testing this logic for some species for genus-level alignments. The added feature will look if the long_read_summary_file (Species-level) exists and is non-empty, use it. The long_read_summary_file_genus will not be used or downloaded. But If it's empty or missing, it exits with 42 and goes to branch 2 triggers the download using the genus file and runs the minimap alignments as usual.
Include links to JIRA tickets
https://www.ebi.ac.uk/panda/jira/browse/ENSGENEBUI-2370
Testing
Have you tested it?
Yes
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