sanger-tol / genomenote

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.
https://pipelines.tol.sanger.ac.uk/genomenote
MIT License
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Add BUSCO to the annotation_statistics subworkflow #141

Open BethYates opened 1 month ago

BethYates commented 1 month ago

Add BUSCO to the annotations statistics subworkflow. To do this you can use the existing nf-core busco module https://nf-co.re/modules/busco/ and run BUSCO in proteins mode. You will need to pass it protein fasta files. Currently the sub-workflow only has a GFF file of the protein annotations, we can use this to produce the fasta files by using https://nf-co.re/modules/gffread/ and the genomic fasta file.

The BUSCO score should be added to the final file output by the subworkflow.