kfukuta/wf-transcriptomes-v202
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wf-transcriptomes-v202/CHANGELOG.md
Sarah Griffiths 5df7e3c2cd template updates
2023-05-09 10:09:33 +00:00

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Changelog

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.

[unreleased]

Changed

  • LICENSE to Oxford Nanopore Technologies PLC. Public License Version 1.0.

[v0.1.10]

Changed

  • Condition sheet parameter description fixed to CSV
  • Update fastqingress

[v0.1.9]

Changed

  • Simplify JAFFAL docs

[v0.1.8]

Changed

  • Description in manifest

[v0.1.7]

Changed

  • -profile conda is no longer supported, users should use -profile standard (Docker) or -profile singularity instead
  • nextflow run epi2me-labs/wf-transcriptomes --version will now print the workflow version number and exit
  • Use parameter --transcriptome-source to define precalculated, reference-based or denovo

[v0.1.6]

Changed

  • Removed sanitize option
  • Reduce size of differential expression data.

Added

  • Improved DE explanation in docs
  • Option to turn off transcript assembly steps with param transcript_assembly

Fixed

  • 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.

[v0.1.5]

Added

  • Differential transcript and gene expression subworkflow

[v0.1.4]

Added

  • JAFFAL fusion detection subworkflow

Changed

  • 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

[v0.1.3]

Changed

  • Better help text on cli
  • Use EPI2ME Labs-maintained version of pychopper

[v0.1.2]

Added

  • direct_rna option
  • Some extra error handling
  • Minor report display improvements

[v0.1.1]

Fixed

  • 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

[v0.1.0]

Added

  • Added the denovo pipeline

Changed

  • Updates to the report plots

[v0.0.1]

Added