From 19ecf0040391d83d6df2fe4b329710a65193a70f Mon Sep 17 00:00:00 2001 From: subwaystation Date: Thu, 14 Mar 2024 11:13:15 +0100 Subject: [PATCH] prepare 1.1.1 release --- CHANGELOG.md | 8 +++++++- README.md | 2 ++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 4 files changed, 12 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c2b4f13..83b8304 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,7 +2,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## 1.2.0dev - LATÜRNICH +## 1.1.1 - LATÜRNICH + +This release fixes some important bugs: + +- Per default, we set the number of mappings in `wfmash` to `1`. Previously, this was set to the given number of haplotypes. +- To complement the issue above, there is a new parameter `wfmash_n_mappings` with default `1`. +- `bcftools` in the `VG_DECONSTRUCT` module was updated to the most recent version `1.19` to prevent errors like `corrupted size vs. prev_size`. ## 1.1.0 - Schmuddlweddr diff --git a/README.md b/README.md index 722779e..796efed 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,8 @@ [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pangenome-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pangenome)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +> WARNING: Version 1.1.0 does contain some known bugs. It is recommended to directly use version 1.1.1. For details please take a look at [CHANGELOG.md](CHANGELOG.md). + ## Introduction **nf-core/pangenome** is a bioinformatics best-practice analysis pipeline for pangenome graph construction. The pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e3d29f8..c6b5600 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/pangenome + This report has been generated by the nf-core/pangenome analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-pangenome-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index d0d726c..ec06325 100644 --- a/nextflow.config +++ b/nextflow.config @@ -277,7 +277,7 @@ manifest { description = """The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.2.0dev' + version = '1.1.1' doi = 'https://doi.org/10.5281/zenodo.8202636' }