v4.0

• We incorporated transcriptome_metrics.sh (https://github.com/cfarkas/annotate_my_genomes/blob/master/additional_scripts/transcriptome_metrics.sh) into the pipeline to obtain novel cds and correspondent proteins.
• the pipeline can accept fixed GTF files, related to gpertea/stringtie#270. The script to fix stringtie GTF files is the following: https://gist.github.com/cfarkas/7ec131ad0880acbcc3c31257cdca3f97
• Updated NextFlow scripts.

v3.3

June 28, 2022: Adding Docker run, as depicted here: https://hub.docker.com/r/carlosfarkas/annotate_my_genomes_v3

v3.2

Minor fixes on README and makefile.nf

v3.0

• Nextflow scripts do not rely on binaries
• Updated makefile, now it can be runned on Nextflow
• Adding Nextflow installing instructions on README

v2.1

• Improving conda recipe for FEELnc installation, with better performance in Ubuntu 16.04 LTS, 18.04 LTS and 20.04.3 LTS.
• Tested Nextflow scripts in all Ubuntu distros
• Tested in galGal6, mm10, hg38, danRer11 and ce11.
• fixing bugs in homolog detection (wiki examples)
• adding a stable environment.yml for Nextflow

v2.0

-o option added, fixing input paths and variables, conda stable release. Tested in Ubuntu 16.04 LTS, 18.04, 20.04 LTS

v1.0.3

First stable release, tested in mouse, human, chicken and zebrafish.

v1.0.2

Fix parallel sed script for genes containing ":"

v1.0.1

• Fixed minor bugs in additional scripts

v1.0

• getopts supported
• Successfully tested in mouse and chicken assemblies