193 lines
6.6 KiB
Markdown
193 lines
6.6 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/1.1.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [v1.1.0]
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### Changed
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- Improve documentation around filtering of transcripts done before DTU analysis.
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- Renamed files:
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- `de_analysis/all_counts_filtered.tsv` to `de_analysis/filtered_transcript_counts_with_genes.tsv`
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- `de_analysis/de_tpm_transcript_counts.tsv` to `de_analysis/unfiltered_tpm_transcript_counts.tsv`
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- Minimum memory requirements to `32 GB`.
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### Added
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- Published isoforms table to output directory.
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- Output additional `de_analysis/cpm_gene_counts.tsv` with counts per million gene counts.
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- Output additional `de_analysis/unfiltered_transcript_counts_with_genes.tsv` with unfiltered transcript counts with associated gene IDs.
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- Add gene name column to the de_analysis counts TSV files.
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### Fixed
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- Mapping stage using a single thread only.
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### Changed
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- More memory assigned to the fusion detection process.
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- 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`.
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## [v1.0.0]
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### Added
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- Published minimap2 and pychopper results to output directory.
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- Two extra pychopper parameters `--cdna_kit` and `--pychopper_backend`. `--pychopper_options` is still available to define any other options.
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- Memory requirements for each process.
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### Changed
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- Documentation.
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### Fixed
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- When Jaffa is run only output one report.
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## [v0.4.2]
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### Changed
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- Sample sheet must include a `control` type to indicate which samples are the reference for the differential expression pipeline.
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### Removed
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- Default local executor CPU and RAM limits.
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## [v0.4.1]
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### Changed
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- Updated docker container with Pychopper to support LSK114.
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## [v0.4.0]
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### Fixed
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- Remove dead links from README
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### Removed
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- Denovo `--transcriptome_source` option.
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## [v0.3.1]
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### Added
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- Handling for input reference transcriptome headers that contain `|`
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## [v0.3.0]
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### Changed
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- Improve differential expression outputs.
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- Include transcript and gene count tables in DE_final folder.
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- If differential expression subworkflow is used a non redundant transcriptome will be output which includes novel transcripts.
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- Added wording to the report about how to identify novel transcripts in the DE tables.
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- Nextflow minimum required version to 23.04.2
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- `--minimap_index_opts` parameter has been changed to `minimap2_index_opts` for consistency.
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### Added
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- 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).
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- Wording to the report about how to identify novel transcripts in the DE tables.
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## [v0.2.1]
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### Changed
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- Any sample aliases that contain spaces will be replaced with underscores.
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- Updated documentation to explain we only support Ensembl, NCBI and ENCODE annotation file types.
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### Fixed
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- Documentation parameter examples corrected.
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- Handling for annotation files that use gene as gene_id attribute.
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- Handling for Ensembl annotation files.
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## [v0.2.0]
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### Changed
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- GitHub issue templates
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- Condition sheet is no longer required. The sample sheet is now used to indicate condition instead.
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- For differential expression, the sample sheet must have a `condition` column to indicate which condition group each sample in the sample sheet belongs to.
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- Values for the condition may be any two distinct strings, for example: treated/untreated; sample/control etc.
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### Fixed
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- Remove default of null for `--ref_transcriptome`.
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- Read mapping summary table in the report has correct sample_ids.
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## [v0.1.13]
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### Added
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- Handling for GFF3 reference_annotation file type.
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- Warning for the `--transcriptome_source` denovo pipeline option.
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### Changed
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- Enum choices are enumerated in the `--help` output
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- Enum choices are enumerated as part of the error message when a user has selected an invalid choice
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- Bumped minimum required Nextflow version to 22.10.8
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### Fixed
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- Replaced `--threads` option in fastqingress with hardcoded values to remove warning about undefined `param.threads`
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- Fix for the `--transcriptome_source` denovo pipeline option.
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## [v0.1.12]
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### Added
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- Handling for GFF3 reference_annotation file type.
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- Handling gzip input reference and annotation parameters.
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- Handling for NCBI gtfs that contain some empty transcript ID fields.
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## [v0.1.11]
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### Changed
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- LICENSE to Oxford Nanopore Technologies PLC. Public License Version 1.0.
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### Added
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- Configuration for running demo data in AWS
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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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