v0.3.1

leafworker (v0.3.1)

This patch release of leafworker applies an important patch to IsoformSwitchAnalyzeR to prevent incorrect type casting in design matrices, resolving potential rank issues during analysis. It also updates the output directory structure for Salmon count matrices to explicitly include the batch ID. This new option can be supplied to prevent overwriting of jointly-called files across runs of the pipeline.

Bug fixes:

• IsoformSwitchAnalyzeR Patch: Applied a runtime patch to IsoformSwitchAnalyzeR's importRdata function to prevent automatic type casting of numeric/integer columns in the design matrix. This resolves an issue where auto-casting could cause the design matrix to become non-full rank (related to IsoformSwitchAnalyzeR issue #247).
• Salmon Output Path: Updated the output paths for Salmon quantification matrices (raw_counts.tsv and tpm_normalized.tsv) to include the batch_id in the directory structure. This ensures outputs are correctly organized by different runs or downstream analysis batches of the pipeline.

Full Changelog: v0.3.0...v0.3.1

v0.3.0

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: v0.2.0...v0.3.0

v0.2.0

leafworker (v0.2.0)

Feature: Add in a step to run IsoformSwitchAnalyzeR with or without covariates to find differential isoform usage/switching.

• Adding new rule to generate leafviz Rdata file.
• Adding new docker image with IsoformSwitchAnalyzeR dependencies.
• Adding docker image with ISA dependencies.
• Adding bam2fq step for running salmon, step to build salmon index, salmon-quant step, step to create a raw and normalized counts matrix, and a step to run ISA
• Adding quantify transcripts option to conditionally run IsoformSwitchAnalyzeR

Big fixes:

• Unset any R-related ENV vars related to system-level and user-level R package installations
• Updating renaming of col names for ISA sample sheet

Full Changelog: v0.1.0...v0.2.0

v0.1.0

leafworker (v0.1.0)

This is the first public release of leafworker. This release marks a significant milestone in the development of leafworker.

About

Leafworker was designed to simplify the process of running leafcutter on hundreds or thousands of samples. It was designed to be highly scalable and reproducible. This release implements all the upstream data-processing steps for running leafcutter, and it performs leafcutter's differential splicing analysis. If you use leafworker, please don't forget to cite leafcutter. This pipeline is a wrapper around the leafcutter, a tool for the analysis of RNA-seq data to identify and quantify alternative splicing events.

Full Changelog: https://github.com/OpenOmics/leafworker/commits/v0.1.0