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Releases: ConesaLab/SQANTI3

Release v6.0.1

24 Apr 09:57
@pabloati pabloati
v6.0.1
1cd5f51

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Release v6.0.1 Latest
Latest

What's Changed

New Contributors

Full Changelog: v6.0...v6.0.1

Contributors

pabloati, TianYuan-Liu, and 2 other contributors
Assets 3
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Release 6.0

31 Mar 10:33
@pabloati pabloati
v6.0
47602ab

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Release 6.0

Explanation

This is a major release of SQANTI3. The fundamental changes revolt around the rescue module, with some changes to the order and structure of the QC classification table.

SQANTI3 QC module

There has been an adition of the outputs from TD2 into the classification file, such as the Psauron score, the type of CDS and the protein length. Some columns have been rearranged, to have a more logical order (subcategory goes after structural_category). Internal changes have been done to the classess that handle the isoforms during the workflow, but this will not impact the user experience, only facilitate development and speed.

Several aspects of the classification table have been optimized. The columns of diff_to_TTS and diff_to_TSS have been changed so they show the nucleotide distance of the "spliced" transcripts, and two new columns have been added to show the genomic distance of the TSS/TTS of the isoforms (diff_to_TT/SS_genomic). As well, the ref_legnth and ref_exons columns have been set to NA for non-FSM/ISM transcripts, since they have no reference associated (before the value that was being shown was that of the best reference match)

New plots have been incuded in the report, to take advantage of the information that TD2 outputs, in comparison with GMST.

SQANTI3 Filter module

Minor changes have been introduced here, mainly bugfixes and validation of the categoruies in the rule filter

SQANTI3 Rescue module

The logic behind rescue has been altered, specially when it comes to the rescue-by-mapping pipeline. Now, the best isoform hit will be selected based on the alignment score that minimap2 produces. This will guide the selection of the rescued isoform.

The requantification module has been fully implemented into the code. The couns fo the artifact will be added to the counts of either their best matching isoform (either from the reference or from the long-reads defined transcriptome) or to the Transcirpt Divergency. For more information on the logic, process and results, please visit the wiki, where the pipeline is explained in detail.

SQANTI reads

Quality of life improvements have been introduced, to make clearer for the user the different arguments of SQANTI-reads

What's Changed

New Contributors

Full Changelog: v5.5.4...v6.0

Contributors

fmerinocasallo, carolinamonzo, and 2 other contributors
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Release v6.0-beta

03 Feb 13:49
@pabloati pabloati
v6.0-beta
ab1a3bc

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Release v6.0-beta Pre-release
Pre-release

THIS IS A PRE-RELEASE TO TEST THE NEW FUNCTIONALITY OF SQANTI3.

Explanation

This is a major release of SQANTI3. The fundamental changes revolt around the rescue module, with some changes to the order and structure of the QC classification table.

SQANTI3 QC module

There has been an adition of the outputs from TD2 into the classification file, such as the Psauron score, the type of CDS and the protein length. Some columns have been rearranged, to have a more logical order (subcategory goes after structural_category). Internal changes have been done to the classess that handle the isoforms during the workflow, but this will not impact the user experience, only facilitate development and speed.

New plots have been incuded in the report, to take advantage of the information that TD2 outputs, in comparison with GMST.

SQANTI3 Filter module

Minor changes have been introduced here, mainly bugfixes and validation of the categoruies in the rule filter

SQANTI3 Rescue module

The logic behind rescue has been altered, specially when it comes to the rescue-by-mapping pipeline. Now, the best isoform hit will be selected based on the alignment score that minimap2 produces. This will guide the selection of the rescued isoform.

The requantification module has been fully implemented into the code. The couns fo the artifact will be added to the counts of either their best matching isoform (either from the reference or from the long-reads defined transcriptome) or to the Transcirpt Divergency. For more information on the logic, process and results, please visit the wiki, where the pipeline is explained in detail.

SQANTI reads

Quality of life improvements have been introduced, to make clearer for the user the different arguments of SQANTI-reads

What's Changed

Full Changelog: v5.5.1...v6.0

Full Changelog: v5.5.4...v6.0-alpha

Contributors

carolinamonzo, pabloati, and TianYuan-Liu
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Release v5.5.4

04 Dec 11:21
@pabloati pabloati
v5.5.4
093898f

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Release v5.5.4

Release aiming at fixing two main issues:

  1. In the case of having duplicated isoform and reference IDs rescue could crash (some tools like Bamboo or Flair assing the name of the refence to the isoforms in the transcriptome if a perfect match is found)
  2. In the parallelization, the isoform_hits option was bugged, as well as a small bug with the corruption of a header in the abundance calculation.

What's Changed

  • Add disk space cleanup to DockerHub release workflow by @Copilot in #549
  • parallel issue fixed by @pabloati in #557
  • Fixed parallelization isoforms_hits by @pabloati in #560
  • Optimize GitHub Actions workflows with path filters and caching by @Copilot in #558

Full Changelog: v5.5.3...v5.5.4

Contributors

pabloati
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Release v5.5.3

20 Nov 14:55
@pabloati pabloati
v5.5.3
ba567d8
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Release v5.5.3

Quick release to fix some important issues that arose in SQANTI3 in the last days. The next release (hopelfuly) will implement major changes in the pipeline!

What's Changed

  • Bugfix/rescue duplications 545 by @pabloati in #546
  • Fix to saturation plots failing when isoforms lacked counts by @pabloati in #548
  • Fix to the abundance count pipeline in the parallel mode, pointed out by #556 by @pabloati

Full Changelog: v5.5.2...v5.5.3

Contributors

pabloati
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Release v5.5.2

13 Nov 17:16
@pabloati pabloati
v5.5.2
9c23196
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Release v5.5.2

Bugfix release aimed at fixing minor error in the filter report, compilation of conda packages and testing and the classification file

What's Changed

New Contributors

Full Changelog: v5.5.1...v5.5.2

Contributors

fairliereese, pabloati, and 3 other contributors
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Release v5.5.1

04 Aug 10:43
@pabloati pabloati
v5.5.1
c3034fc
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Release v5.5.1

Minor bugfixes from previous version plus a conda environment upgrade

What's Changed

Full Changelog: v5.5...v5.5.1

Contributors

pabloati and FabianJetzinger
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Release v5.5

23 Jun 08:18
@pabloati pabloati
v5.5
d5cc8f7
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Release v5.5

🛠️ Minor Release

This minor release main change is the subsitution of GeneMarkS-T for TransDecoder2 to predict ORFs. This change was done due to the outdating of GMST and its constant issues that we could not solve. Moreover, some essential bugfixes and QOL improvements have been added to the repository. Read below for more information.

✨ Improvements

  • Automatic detection of @SQ headers in SAM files.
  • Added multiple checks for gene_name attributes in reference annotations when required.
  • Improved error handling in rescue rules when no valid rules are provided.
  • Significantly faster rescue file writing (no shell call overhead).
  • Enhanced output management and reduced type errors in filterML.

🐞 Bugfixes

  • Fixed logging: missing files now raise appropriate warnings or errors.
  • Boolean values in the config file are now correctly detected by the wrapper.
  • IsoAnnotLite now checks for the gene_name attribute in the reference.
  • Fixed rescue output generation when no GTF is provided.
  • Custom TP/TN sets and remove_columns in filterML are now handled correctly.
  • SQANTI-reads adapted to the updated argument parser.
  • Fixed string conversion issue in myQueryTranscripts.__str__() when printing None.
  • TSS ratio counts have been corrected.
  • CDS prediction bugs fixed.
  • Fixed IO handling and logging behaviors.

🔧 Changes

  • GMST has been replaced by TD2.
  • SQANTI-reads updated to use the new argument format.
  • Output filenames for CDS predictions have been made more descriptive.
  • Examples updated for consistency with the new version.
  • Rescue script reverted to its previous argument style.

📌 What's Changed (from PRs)

🙌 New Contributor

🔗 Full Changelog: v5.4...v5.5

Contributors

diekhans, pabloati, and 2 other contributors
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Release 5.4

23 Apr 13:00
@pabloati pabloati
v5.4
7ae74e1
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Release 5.4

Introduction

This release introducessignificant changes in SQANTI3.

  1. 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.
  2. 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
  3. 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
  4. 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
  5. Fixed many bugs that were found along the way. See commits and pull requests for more info

What's Changed

New Contributors

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

Contributors

eltociear, Fabian-RY, and 2 other contributors
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v5.3.6

17 Feb 14:53
@pabloati pabloati
v5.3.6
5f182ae
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v5.3.6

What's Changed

  • Update sqanti3_filter.py by @sbresnahan in #397
  • Updated the fl count parser to accept floats in single samples by @pabloati in #406
  • Input file processing upgraded to accept any kind og GTF by @pabloati in #407
  • Fixed report to accept classification with junction types missing by @pabloati in #408
  • Issue 390, pallete and flair input fixed by @pabloati in #412
  • GMST directory saved after parallelization by @pabloati in #414
  • Fixed bug where the isoform hits file was not being propperly created and the flag killed the process, as in issue 431
  • Release 5.3.6 update by @pabloati in #415

New Contributors

Full Changelog: v5.3.5...v5.3.6

Contributors

pabloati and sbresnahan
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