Merge pull request #185 from subwaystation/dev

prepare 1.1.1 release

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
 

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.

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/pangenome/tree/dev" target="_blank">nf-core/pangenome</a>
+  This report has been generated by the <a href="https://github.com/nf-core/pangenome/releases/tag/1.1.1" target="_blank">nf-core/pangenome</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/pangenome/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/pangenome/1.1.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-pangenome-methods-description":
     order: -1000

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'
 }