From e83c92a0e5a9c134122bce2531365a310fda15a0 Mon Sep 17 00:00:00 2001 From: Sarah Griffiths Date: Fri, 1 Aug 2025 15:02:39 +0000 Subject: [PATCH] tag v1.7.1 --- CHANGELOG.md | 9 ++++----- nextflow.config | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 903dba1..a71a16d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [Unreleased] +## [v1.7.1] ### Changed - 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. - 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. - - 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. +- 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. ### Fixed - 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 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 - `values in 'transcripts$tx_strand' must be "+" or "-"`. - 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] ### Changed diff --git a/nextflow.config b/nextflow.config index 70a891a..d41a6fb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -107,7 +107,7 @@ manifest { description = 'Transcriptome analysis including differential expression as well as assembly and annotation of cDNA and direct RNA sequencing data.' mainScript = 'main.nf' nextflowVersion = '>=23.04.2' - version = 'v1.7.0' + version = 'v1.7.1' } epi2melabs {