Release Release 5.4 · ConesaLab/SQANTI3

Introduction

This release introducessignificant changes in SQANTI3.

Introduciton of a loggin system --> Now, all theouptut to the console is controlled via a python logger. The external tools log is redirected to their respective files in the directory logs of each run.
Creation of a wrapper and a config file to run SQANTI3. This wrapper now works via a config file, thus some arguments and the way the parser works have been changed to be adapted to the wrapper
Reestructurarion of the filter module. Most of its scripts have been pythonized and the internal organization has been changed, with modifications to the file namings
Reestructuration of rescue module. Similar to filter, with most of the scirpts changed from R to python, eliminating many calls to external tools or the terminal
Fixed many bugs that were found along the way. See commits and pull requests for more info

Adition of the wrapper to SQANTI by @pabloati in #392
Junctions classification issue fixed by @pabloati in #398
Bugfix/gtf order by @pabloati in #399
Logger by @pabloati in #400
Tests/junctions processing by @pabloati in #401
Github actions: test docker build each commit, and publish to dockerhub on release by @Fabian-RY in #418
Conda testing by @Fabian-RY in #419
FIX: conda change in latest docker failed by @Fabian-RY in #420
Switch attribute parser to regex by @SwiftSeal in #423
Size one cake peak fix by @pabloati in #430
Bugfix/sqanti reads by @pabloati in #432
Bugfix/sqanti reads paula by @pabloati in #435
Filter restructuration by @pabloati in #436
docs: update README.md by @eltociear in #438
Bugfix/gff isoannot by @pabloati in #439
Rescue reorganization by @pabloati in #449
Qc report by @pabloati in #450
Fixed issue 444 by @pabloati in #451
Logger filesystem by @pabloati in #453
Releases/v5.4 by @pabloati in #454

Full Changelog: v5.3.6...v5.4