leafworker (v0.3.0)

This release significantly enhances differential splicing analysis by adding detailed gene, transcript, and exon annotations to Leafcutter results. It also introduces new functionality to generate FASTA sequences for transcripts identified with significant isoform switches in the IsoformSwitchAnalyzeR workflow.

Features

• Enhanced Leafcutter Annotation:

  • Added a new annotation step to the Leafcutter workflow.
  • Results are now annotated with detailed transcript and exon information (gene IDs, transcript IDs, exon numbers, etc.).
  • Added new output file: leafcutter_annotated_results.tsv which merges effect sizes, cluster significance, and additional splicing annotation information.
  • New helper scripts added: exon_annotation.py, splicing_annotation.py, intron_annotation.R, and leafcutter_annotation.py

• IsoformSwitchAnalyzeR Improvements:

  • Added a new rule isoformswitchanalyzer_isoformfasta to generate a FASTA file containing sequences for isoforms with significant switches.
  • Added script isoform_sequences.py extracts transcript sequences for genes with significant isoform switches.

Chores

• Cluster Configuration: Reduced the default wall time for the main job submission script (src/run.sh) from 10 days to 7 days. This aligns with the new max wall time on Skyline.
• Documentation: Updated README.md to explicitly mention IsoformSwitchAnalyzeR support and added its citation reference.

Full Changelog: https://github.com/OpenOmics/leafworker/compare/v0.2.0...v0.3.0