Tags

2.4.0

- New: egne-ep.sh: add --profile and --outdir parameters
- New: new statistics output files (gene coverage, multimapping stats)
- New: specific Helixer parameters for fungi/vertebrate and invertebrate (authors provided)
- Fix: locus_tag_prefix to locustag_prefix
- Fix: make pipeline compliant with "process.scratch = true" for slow filesystems
- Fix: independent_strand_annotation=false
- Update: change main script egn-ep.nf to main.nf

2.3.0

New: Use of mfannot to annotate organelles
New: abinitio ncRNA (tRNA, rRNA, ncRNA) are added at the end of the process (no more used by EuGene sensors)
New: experimental repeat detection (--use_fastrepeat)
New: utility script to retrieve test datasets
Removed: USEARCH option
Update: gmap number of path is a specific parameter
Update: update INFERNAL version
Update: simplify proteic db parameters
Fix: code cleaning, optimisation and compliant with nextflow 25.10

2.2.1

New EuGene version (v5.0.0)
New Helixer training option (--training_use_helixer)
No more need of proteic databases if use of Helixer for training step
Fix utils issues

2.1.1

Add possibility to overwrite EuGene Sensor Plugin templates

2.1.0

- masked genome management
- use of miniprot as default for DB reduction step
- update busco version

2.0.4

2.0.3

2.0.2

2.0.1

2.0.0

Complete pipeline validated on H. annuus species with usearch and without repbase

20220705-#2

Refactoring step #2

1.0.0

Complete process ok, tested on Dsans
Some process are still not cached preventing -resume

0.0.1

First release end-to-end. Issue on --skip_red