This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.
This script will take a ToL organism ID, select the most likely genome FASTA, and associated files. If the expected files are not present on /lustre, it will throw an error and exit.
For this pipeline, it involves finding the merged alignment CRAM along with the unmasked genome file.
Description of feature
This script will take a ToL organism ID, select the most likely genome FASTA, and associated files. If the expected files are not present on
/lustre, it will throw an error and exit.For this pipeline, it involves finding the merged alignment CRAM along with the unmasked genome file.