All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- Removed sanitize option
- Reduce size of differential expression data.
- Improved DE explanation in docs
- Option to turn off transcript assembly steps with param transcript_assembly
- Fix JAFFAL terminating workflow when no fusions found.
- Error if condition sheet and sample sheet don't match.
- Failed to plot DE graphs when one of data sets is 0 length.
- Differential transcript and gene expression subworkflow
- JAFFAL fusion detection subworkflow
- Args parser for fastqingress
- Set out_dir option type to ensure output is written to correct directory on Windows
- Skip unnecessary conversion to fasta from fastq
- Fastqingress metadata map
- Changed workflow name to wf-transcriptomes
- Better help text on cli
- Use EPI2ME Labs-maintained version of pychopper
- direct_rna option
- Some extra error handling
- Minor report display improvements
- Incorrect numbers and of transcripts caused by merging gff files with same gene and transcript ids
- Error handling in de novo pipeline. Skip clusters in build_backbones that cause an isONclust2 error
- Several small fixes in report plotting
- Added the denovo pipeline
- Updates to the report plots
- First release
- Initial port of Snakemake WF from https://github.com/nanoporetech/pipeline-nanopore-ref-isoforms