Merge pull request #193 from subwaystation/dev

bump to 1.1.2 - canguro

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 - canguro
+## 1.1.2 - canguro
+
+This release reverts the `wfmash` tool version to 0.10.4, because the current releases are unstable, not documented, and I don't understand how to set the parameters properly.
+It is currently unclear, when a new _stable_ release will become available. People like @baozg or @AndreaGuarracino are evaluating.
+
+- Per default, we set the number of mappings in `wfmash` to `--n_haplotypes - 1`. Previously, this was set to `1`.
+- Deactivated parameter `wfmash_hg_filter_ani_diff`, because the older `wfmash` version does not support it.
 
 ## 1.1.1 - LATÜRNICH
 

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/1.1.2" 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/1.1.2/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         = '1.1.2'
     doi             = 'https://doi.org/10.5281/zenodo.8202636'
 }