84 lines
2.4 KiB
Markdown
84 lines
2.4 KiB
Markdown
# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [unreleased]
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### Changed
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- LICENSE to Oxford Nanopore Technologies PLC. Public License Version 1.0.
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## [v0.1.10]
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### Changed
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- Condition sheet parameter description fixed to CSV
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- Update fastqingress
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## [v0.1.9]
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### Changed
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- Simplify JAFFAL docs
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## [v0.1.8]
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### Changed
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- Description in manifest
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## [v0.1.7]
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### Changed
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- `-profile conda` is no longer supported, users should use `-profile standard` (Docker) or `-profile singularity` instead
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- `nextflow run epi2me-labs/wf-transcriptomes --version` will now print the workflow version number and exit
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- Use parameter `--transcriptome-source` to define precalculated, reference-based or denovo
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## [v0.1.6]
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### Changed
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- Removed sanitize option
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- Reduce size of differential expression data.
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### Added
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- Improved DE explanation in docs
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- Option to turn off transcript assembly steps with param transcript_assembly
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### Fixed
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- Fix JAFFAL terminating workflow when no fusions found.
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- Error if condition sheet and sample sheet don't match.
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- Failed to plot DE graphs when one of data sets is 0 length.
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## [v0.1.5]
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### Added
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- Differential transcript and gene expression subworkflow
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## [v0.1.4]
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### Added
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- JAFFAL fusion detection subworkflow
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### Changed
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- Args parser for fastqingress
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- Set out_dir option type to ensure output is written to correct directory on Windows
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- Skip unnecessary conversion to fasta from fastq
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- Fastqingress metadata map
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- Changed workflow name to wf-transcriptomes
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## [v0.1.3]
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### Changed
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- Better help text on cli
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- Use EPI2ME Labs-maintained version of pychopper
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## [v0.1.2]
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### Added
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- direct_rna option
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- Some extra error handling
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- Minor report display improvements
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## [v0.1.1]
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### Fixed
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- Incorrect numbers and of transcripts caused by merging gff files with same gene and transcript ids
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- Error handling in de novo pipeline. Skip clusters in build_backbones that cause an isONclust2 error
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- Several small fixes in report plotting
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## [v0.1.0]
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### Added
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- Added the denovo pipeline
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### Changed
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- Updates to the report plots
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## [v0.0.1]
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### Added
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- First release
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- Initial port of Snakemake WF from https://github.com/nanoporetech/pipeline-nanopore-ref-isoforms
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