sanger-tol/treeval: 1.4.4 - Ancient Hippaforalkus (H4)

Our 11th release for sanger-tol/treeval.

Enhancements & Fixes

• Replaced the TELO_FINDER subworkflow with the SANGER-TOL/TELO_FINDER
• By request, added split telomere ingestion to have the 5 and 3 prime directions separately displayable in Pretext. This, by default, is set to false.
• Updated the code in PRETEXT_GRAPH to handle the new telo input, which may be split, whole or both.
• In split mode, the whole telomere will also be ingested.
• Reference input can now be gzipped.
• Moved the GAWK_UPPER_SEQUENCE module into the workflow main.nf file from the telomere subworkflow.
• Updated list for modes that run synteny.
• Removed redundant groovy.
• Fix for params not correctly running various components of the pipeline.
• GAWK_SPLIT_TELOMERE has been updated to use the nf-core module rather than a slightly custom local version.

Full Changelog: https://github.com/sanger-tol/treeval/compare/1.4.3...1.4.4