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CHANGELOG.md

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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

  • MA plot in the results_dge.pdf has been updated to match the MA plot in the report.

[v1.1.1]

Changed

  • Improved handling of different annotation file types (eg. .gtf/.gff/.gff3) in de_analysis mode.
  • Improved handling of annotation files that do not contain version numbers in transcript_id (such as gtf's from Ensembl).

Fixed

  • Differential expression failing with 10 or more samples.
  • Regression causing the DE analysis numeric parameters to not be evaluated correctly.

[v1.1.0]

Changed

  • Improve documentation around filtering of transcripts done before DTU analysis.
  • Renamed files:
    • de_analysis/all_counts_filtered.tsv to de_analysis/filtered_transcript_counts_with_genes.tsv
    • de_analysis/de_tpm_transcript_counts.tsv to de_analysis/unfiltered_tpm_transcript_counts.tsv
  • Minimum memory requirements to 32 GB.

Added

  • Published isoforms table to output directory.
  • Output additional de_analysis/cpm_gene_counts.tsv with counts per million gene counts.
  • Output additional de_analysis/unfiltered_transcript_counts_with_genes.tsv with unfiltered transcript counts with associated gene IDs.
  • Add gene name column to the de_analysis counts TSV files.

Fixed

  • Mapping stage using a single thread only.

Changed

  • More memory assigned to the fusion detection process.
  • When no --ref_annotation is provided the workflow will still run but the output transcripts will not be annotated. However --de_analysis mode still requires a --ref_annotation.

[v1.0.0]

Added

  • Published minimap2 and pychopper results to output directory.
  • Two extra pychopper parameters --cdna_kit and --pychopper_backend. --pychopper_options is still available to define any other options.
  • Memory requirements for each process.

Changed

  • Documentation.

Fixed

  • When Jaffa is run only output one report.

[v0.4.2]

Changed

  • Sample sheet must include a control type to indicate which samples are the reference for the differential expression pipeline.

Removed

  • Default local executor CPU and RAM limits.

[v0.4.1]

Changed

  • Updated docker container with Pychopper to support LSK114.

[v0.4.0]

Fixed

  • Remove dead links from README

Removed

  • Denovo --transcriptome_source option.

[v0.3.1]

Added

  • Handling for input reference transcriptome headers that contain |

[v0.3.0]

Changed

  • Improve differential expression outputs.
  • Include transcript and gene count tables in DE_final folder.
  • If differential expression subworkflow is used a non redundant transcriptome will be output which includes novel transcripts.
  • Added wording to the report about how to identify novel transcripts in the DE tables.
  • Nextflow minimum required version to 23.04.2
  • --minimap_index_opts parameter has been changed to minimap2_index_opts for consistency.

Added

  • An additional gene name column to the differential gene expression results. This is especially handy for transcriptomes where the gene ID is not the same as gene name (e.g. Ensembl).
  • Wording to the report about how to identify novel transcripts in the DE tables.

[v0.2.1]

Changed

  • Any sample aliases that contain spaces will be replaced with underscores.
  • Updated documentation to explain we only support Ensembl, NCBI and ENCODE annotation file types.

Fixed

  • Documentation parameter examples corrected.
  • Handling for annotation files that use gene as gene_id attribute.
  • Handling for Ensembl annotation files.

[v0.2.0]

Changed

  • GitHub issue templates
  • Condition sheet is no longer required. The sample sheet is now used to indicate condition instead.
    • For differential expression, the sample sheet must have a condition column to indicate which condition group each sample in the sample sheet belongs to.
    • Values for the condition may be any two distinct strings, for example: treated/untreated; sample/control etc.

Fixed

  • Remove default of null for --ref_transcriptome.
  • Read mapping summary table in the report has correct sample_ids.

[v0.1.13]

Added

  • Handling for GFF3 reference_annotation file type.
  • Warning for the --transcriptome_source denovo pipeline option.

Changed

  • Enum choices are enumerated in the --help output
  • Enum choices are enumerated as part of the error message when a user has selected an invalid choice
  • Bumped minimum required Nextflow version to 22.10.8

Fixed

  • Replaced --threads option in fastqingress with hardcoded values to remove warning about undefined param.threads
  • Fix for the --transcriptome_source denovo pipeline option.

[v0.1.12]

Added

  • Handling for GFF3 reference_annotation file type.
  • Handling gzip input reference and annotation parameters.
  • Handling for NCBI gtfs that contain some empty transcript ID fields.

[v0.1.11]

Changed

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

Added

  • Configuration for running demo data in AWS

[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