Implementation of IsoformSwitchAnalyzeR

CHANGELOG.md

@@ -3,6 +3,15 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.0.5 - 2024-06-04
+
+- Added IsoformSwitchAnalyzeR to pipeline.
+- Updated to migrate from nf-validation to nf-schema.
+
+## v1.0.4 - 2024-04-21
+
+- Fixed incorrect assignment of cluster groups (Issue #131).
+
 ## v1.0.3 - 2024-02-23
 
 - Improved TPM file splitting performance (Issue #120).

CITATIONS.md

@@ -81,6 +81,12 @@
 
   > Nowicka M, Robinson MD (2016). “DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics [version 2; referees: 2 approved].” F1000Research, 5(1356). doi: 10.12688/f1000research.8900.2.
 
+- [IsoformSwitchAnalyzeR](https://www.bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html)
+
+  > Vitting-Seerup K, Sandelin A (2017). “The Landscape of Isoform Switches in Human Cancers.” Mol. Cancer Res. doi:10.1158/1541-7786.MCR-16-0459, doi: 10.1158/1541-7786.MCR-16-0459.
+
+  > Vitting-Seerup K, Sandelin A (2019). “IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences.” Bioinformatics. doi:10.1093/bioinformatics/btz247, doi: 10.1093/bioinformatics/btz247.
+
 - [edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html)
 
   > Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140. doi: 10.1093/bioinformatics/btp616.

README.md

@@ -38,6 +38,8 @@
     1. [`Salmon`](https://combine-lab.github.io/salmon/) -> [`DRIMSeq`](https://bioconductor.org/packages/release/bioc/html/DRIMSeq.html) -> [`DEXSeq`](https://f1000research.com/articles/7-952)
     2. Filtering with [`DRIMSeq`](https://bioconductor.org/packages/release/bioc/html/DRIMSeq.html)
     3. Differential transcript usage with [`DEXSeq`](https://bioconductor.org/packages/devel/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html)
+    4. [`Salmon`](https://combine-lab.github.io/salmon/) -> [`IsoformSwitchAnalyzeR`](https://www.bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html)
+    5. Isoform switch analysis with [`IsoformSwitchAnalyzeR`](https://www.bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html)
 12. Event-based splicing analysis:
     1. [`STAR`](https://github.com/alexdobin/STAR) -> [`rMATS`](https://github.com/Xinglab/rmats-turbo)
     2. [`Salmon`](https://combine-lab.github.io/salmon/) -> [`SUPPA2`](https://github.com/comprna/SUPPA)
@@ -104,7 +106,7 @@ nf-core/rnasplice was originally written by the bioinformatics team from [Zifo R
 - [Asma Ali](https://github.com/asmaali98)
 - [Lathika Madhan Mohan](https://github.com/lathikaa)
 
-We thank Harshil Patel ([@drpatelh](https://github.com/drpatelh)) and Seqera Labs ([seqeralabs](https://github.com/seqeralabs)) for their assistance in the development of this pipeline.
+We thank Harshil Patel ([@drpatelh](https://github.com/drpatelh)), Seqera Labs ([seqeralabs](https://github.com/seqeralabs)) and Jesse Angelis ([@jesseangelis](https://github.com/jesseangelis)) for their assistance in the development of this pipeline.
 
 <img src="docs/images/zifo_logo.jpg" alt="Zifo RnD Solutions" width="200"/>
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/rnasplice/releases/tag/1.0.3" target="_blank">nf-core/rnasplice</a>
+  This report has been generated by the <a href="https://github.com/nf-core/rnasplice/releases/tag/1.0.5" target="_blank">nf-core/rnasplice</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/rnasplice/1.0.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/rnasplice/1.0.5/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-rnasplice-methods-description":

assets/schema_input.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/rnasplice/master/assets/schema_input.json",
     "title": "nf-core/rnasplice pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",