From 98bf8bb325d1abc72b0d877cb559278542c1c139 Mon Sep 17 00:00:00 2001
From: d4straub <daniel.straub@uni-tuebingen.de>
Date: Thu, 25 Jul 2024 14:34:14 +0200
Subject: [PATCH 1/3] nf-core bump-version 2.11.0

---
 assets/multiqc_config.yml | 4 ++--
 nextflow.config           | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index ec828d82..57691707 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/ampliseq/tree/dev" target="_blank">nf-core/ampliseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/ampliseq/releases/tag/2.11.0" target="_blank">nf-core/ampliseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/ampliseq/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/ampliseq/2.11.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-ampliseq-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 32729b03..f81c0033 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -357,7 +357,7 @@ manifest {
     description     = """Amplicon sequencing analysis workflow using DADA2 and QIIME2"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.11.0dev'
+    version         = '2.11.0'
     doi             = '10.5281/zenodo.1493841,10.3389/fmicb.2020.550420'
 }
 

From 6de1d0dabd3c98024bfc6042e99a089d5fc60143 Mon Sep 17 00:00:00 2001
From: d4straub <daniel.straub@uni-tuebingen.de>
Date: Thu, 25 Jul 2024 14:34:30 +0200
Subject: [PATCH 2/3] update CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d0b34107..a40ff833 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## nf-core/ampliseq version 2.11.0dev
+## nf-core/ampliseq version 2.11.0 - 2024-08-06
 
 ### `Added`
 

From a3e82844a5c3fdaba25643bb5fbcd43a54c6393a Mon Sep 17 00:00:00 2001
From: d4straub <daniel.straub@uni-tuebingen.de>
Date: Thu, 25 Jul 2024 14:34:53 +0200
Subject: [PATCH 3/3] fix typo in report

---
 assets/report_template.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/assets/report_template.Rmd b/assets/report_template.Rmd
index a1bc6b4b..76119739 100644
--- a/assets/report_template.Rmd
+++ b/assets/report_template.Rmd
@@ -1544,7 +1544,7 @@ for (folder in ancom) {
 any_ancombc <- !isFALSE(params$ancombc) || !isFALSE(params$ancombc_formula)
 ```
 
-```{r, eval = !isFALSE(params$any_ancombc), results='asis'}
+```{r, eval = !isFALSE(any_ancombc), results='asis'}
 cat(paste0("
 ## ANCOM-BC