SQANTI 5.3.0

This release include some new minor features, such as the inclusion of a Dockerfile of sqanti and a wrapper to execute all SQANTI steps at once. Also enhances compatibility for fastq.gz files in sqanti3_qc.py and a new sqanti tool, sqanti_reads.py!

Several bugfixes are corrected: Sqanti QC report is now more robust in absence of some categories of transcripts and transcripts with unknown strands are redirected to an external file to inform the user about possible problems. Full list of changes is below

What's Changed

• Sqanti reads by @carolinamonzo in #321
• Dockerfile by @Fabian-RY in #323
• Added compatibility for .gz compressed fasta/fastq isoforms to SQANTI3_QC by @Fabian-RY in #326
• Fixes report failing when some some structural categories (mainly FSM, ISM, NIC or NNIC) were missing by @Fabian-RY in #332
• Add NA replacement value for ratio_TSS column in ML Rescue by @aarzalluz in #330
• FIX: corrected unchecked existance of a variable in report when --skipORF is used by @Fabian-RY in #339
• FIX: transcripts without known strands (with '.' strand) are redirected by @Fabian-RY in #336
• Bugfix: corrected the sign in difference to TTS/TSS by @Fabian-RY and @alexpan00 in #337
• FIX: gtf.cds.gff is now created when --chunks options is used by @Fabian-RY in #341
• Sqanti3 wrapper available by @Fabian-RY in #344
• Fix: TSS and TTS now is corrected and documented by @Fabian-RY and @alexpan00 in #345
• Sqanti reads devel by @carolinamonzo in #356
• Fixing stuff for paper revision by @carolinamonzo in #358
• Sqanti reads devel updating environment by @carolinamonzo in #359

New Contributors

• @Fabian-RY made their first contribution in #323

Full Changelog: v5.2.2...v5.3.0

SQANTI3 v5.2.2

Since the latest release, improvements in genic intron e7054ab intergenic and NIC isoform classification have been included a7c2680 Errors in the conda environment generation have been solved and monoexons that don't overlap an entire junction will be considered genic, not NIC. Only when the monoexon spans a whole intron will be considered NIC by intron retention 3275a7f. Also CAGE peak assignation has been improved 52def33.

SQANTI3 v5.2.1

Release Update
We're excited to announce this release, bringing crucial fixes and enhancements to improve your experience:

Bug Fixes:

• Resolved a fatal error in SQANTI3 report generation (Issue #278).
• Resolved the issue with the missing 'howtouse.png' image in the HTML report.

Enhancements:

• Simplified installation by removing the cDNA_Cupcake dependency, thanks to @diekhans (Issue #271).
• Fixed issues with reading STAR junction/coverage files in Squanti3 V 5.2 through update conda environment (Issue #260).
• Corrected an error in generating the Kallisto index through update conda environment (Issue #257).

These updates aim to streamline your workflow and enhance software reliability. We thank our community for their valuable input and support.

SQANTI3 v5.2

Update sqanti3_rescue.py version