Uptaded version to v5.3.0

Dockerfile

@@ -1,18 +1,18 @@
-# Base image for SQANTI3/v5.2.2 with Ubuntu 22.04
+# Base image for SQANTI3/v5.3.0 with Ubuntu 22.04
 
 # Using ubuntu 22.04
 # Right now edlib doesn't work with python 3.12 which is the default version
 # of python in Ubuntu 24.04. edlib has had no updates since April 19, 2023
 # so no compatibility is expected for the time being.
 # Dockerfile originally developed by @skchronicles, updated and optimized
-# for version v5.2.2 by @Fabian-RY
+# for version v5.3.0 by @Fabian-RY
 
 FROM ubuntu:22.04
 SHELL ["/bin/bash", "--login" ,"-c"]
 
 # Set the versions of different softwares dependencies and SQANTI3 version
 # To install
-ENV SQANTI3_VERSION="5.2.2"
+ENV SQANTI3_VERSION="5.3.0"
 ENV DESALT_VERSION="1.5.6"
 ENV NAMFINDER_VERSION="0.1.3"
 
@@ -124,7 +124,7 @@ ENV PATH="${PATH}:/opt2/namfinder/${NAMFINDER_VERSION}/namfinder-${NAMFINDER_VER
 WORKDIR /opt2
 
 ########### SQANTI3 (currentily v${NAMFINDER_VERSION}) ############
-# Installs SQANTI3 with the version defined in the ENV variable (currently 5.2.2)
+# Installs SQANTI3 with the version defined in the ENV variable (currently 5.3.0)
 # dependenciesand requirements have already been
 # satisfied, for more info see:
 # https://github.com/ConesaLab/SQANTI3

README.md

@@ -13,7 +13,7 @@ SQANTI3 is the newest version of the [SQANTI tool](https://www.ncbi.nlm.nih.gov/
 SQANTI3 is the first module of the [Functional IsoTranscriptomics (FIT)](https://tappas.org/) framework, which also includes IsoAnnot and tappAS.
 
 ## Installation
-The [latest SQANTI3 release](https://github.com/ConesaLab/SQANTI3/releases/tag/v5.2.2) (31/07/2024) is **version 5.2.2**. See our wiki for [installation instructions](https://github.com/ConesaLab/SQANTI3/wiki/Dependencies-and-installation).
+The [latest SQANTI3 release](https://github.com/ConesaLab/SQANTI3/releases/tag/v5.3.0) (04/12/2024) is **version 5.3.0**. See our wiki for [installation instructions](https://github.com/ConesaLab/SQANTI3/wiki/Dependencies-and-installation).
 
 For informacion about previous releases and features introduced in them, see the [version history](https://github.com/ConesaLab/SQANTI3/wiki/Version-history).
 
@@ -56,3 +56,4 @@ If you are using SQANTI3 in your research, please cite the following paper in ad
 
 - Pardo-Palacios, F.J., Arzalluz-Luque, A. et al. **SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms**. *Nat Methods* (2024). https://doi.org/10.1038/s41592-024-02229-2
 
+- Keil, N., Monzó, C., McIntyre, L., Conesa, A. **SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments**. BioRxiv (2024) https://www.biorxiv.org/content/10.1101/2024.08.23.609463v2

sqanti3_filter.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 __author__  = "[email protected]"
-__version__ = '5.2.2'  # Python 3.7 syntax!
+__version__ = '5.3.0.'  # Python 3.7 syntax!
 
 """
 New SQANTI3 filter. It will serve as a wrapper for "rules" filter and "Machine-Learning" filter.

sqanti3_qc.py

@@ -5,7 +5,7 @@
 # Modified by Fran ([email protected]) currently as SQANTI3 version (05/15/2020)
 
 __author__  = "[email protected]"
-__version__ = '5.2.2'  # Python 3.7
+__version__ = '5.3.0'  # Python 3.7
 
 import pdb
 import os, re, sys, subprocess, timeit, glob, copy

sqanti3_rescue.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 __author__  = "[email protected]"
-__version__ = '5.2.2'
+__version__ = '5.3.0'
 
 ###################################################
 ##########     SQANTI3 RESCUE WRAPPER    ##########

sqanti3_wrapper.sh

@@ -2,16 +2,14 @@ filter_corrected_gtf#! /bin/bash -xe
 
 # Author: Fabián Robledo
 # Email: [email protected]
-# Version: 0.9.1
+# Version: 1.0.0
 
 # One SQANTI3 to run them all
 # A wrapper, with a config file, to execute al three steps of a sqanti3 pipeline
 # in one execution
 # Al three steps (QC, filter and rescue) can be executed at will , as long
 # as the conf is told to skip the script in question
 
-# EXPERIMENTAL: this Wrapper is in progress, so expect that some parameters 
-# are not perfectly tunned.
 # SQANTI3 (QC, Filter and Rescue) combined
 
 function main () {