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tag v1.7.1

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Sarah Griffiths 2025-08-01 15:02:39 +00:00
parent 7a94b2c515
commit e83c92a0e5
2 changed files with 5 additions and 6 deletions
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9
CHANGELOG.md
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@ -4,23 +4,22 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased] ## [v1.7.1]
### Changed ### Changed
- Updated to wf-template v5.6.2, changing: - Updated to wf-template v5.6.2, changing:
- Reduce verbosity of debug logging from fastcat which can occasionally occlude errors found in FASTQ files during ingress. - Reduce verbosity of debug logging from fastcat which can occasionally occlude errors found in FASTQ files during ingress.
- Log banner art to say "EPI2ME" instead of "EPI2ME Labs" to match current branding. This has no effect on the workflow outputs. - Log banner art to say "EPI2ME" instead of "EPI2ME Labs" to match current branding. This has no effect on the workflow outputs.
- pre-commit configuration to resolve an internal dependency problem with flake8. This has no effect on the workflow. - pre-commit configuration to resolve an internal dependency problem with flake8. This has no effect on the workflow.
- Stringtie updated to v2.2.3, which fixes stalling at transcriptome assembly step. - Stringtie updated to v2.2.3, which fixes stalling at transcriptome assembly step.
- Gffcompare updated to v0.12.6, which fixes issue where ref_gene_id was assigned an nan value. - Gffcompare updated to v0.12.6, which fixes issue where ref_gene_id was assigned an nan value.
### Fixed ### Fixed
- Updated to wf-template v5.6.2, fixing: - Updated to wf-template v5.6.2, fixing:
- dacite.exceptions.WrongTypeError during report generation when barcode is null.
- Sequence summary read length N50 incorrectly displayed minimum read length, it now correctly shows the N50. - Sequence summary read length N50 incorrectly displayed minimum read length, it now correctly shows the N50.
- Sequence summary component alignment and coverage plots failed to plot under some conditions. - Sequence summary component alignment and coverage plots failed to plot under some conditions.
- Error in `deAnalysis` process - `mode(counts) %in% "numeric" is not TRUE` - caused by hyphens in sample sheet aliases. - Error in `deAnalysis` process - `mode(counts) %in% "numeric" is not TRUE` - caused by hyphens in sample sheet aliases.
- Error in `deAnalysis` process - `values in 'transcripts$tx_strand' must be "+" or "-"`. - Error in `deAnalysis` process - `values in 'transcripts$tx_strand' must be "+" or "-"`.
- The workflow will now filter out any unstranded annotations from downstream analysis and log a warning. - The workflow will now filter out any unstranded annotations from downstream analysis and log a warning.
- Output the `results_dexseq.tsv` file when `--de_analysis` enabled. - Missing `results_dexseq.tsv` file when `--de_analysis` enabled.
## [v1.7.0] ## [v1.7.0]
### Changed ### Changed

2
nextflow.config
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@ -107,7 +107,7 @@ manifest {
description = 'Transcriptome analysis including differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.' description = 'Transcriptome analysis including differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.'
mainScript = 'main.nf' mainScript = 'main.nf'
nextflowVersion = '>=23.04.2' nextflowVersion = '>=23.04.2'
version = 'v1.7.0' version = 'v1.7.1'
} }
epi2melabs { epi2melabs {