Prepare release 2.12.0

.nf-core.yml

@@ -23,7 +23,7 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 2.12.0dev
+  version: 2.12.0
 update:
   https://github.com/nf-core/modules.git:
     nf-core:

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 2.12.0dev
+## nf-core/ampliseq version 2.12.0
 
 ### `Added`
 
@@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#785](https://github.com/nf-core/ampliseq/pull/785) - Template update for nf-core/tools version 3.0.2
+- [#785](https://github.com/nf-core/ampliseq/pull/785),[#795](https://github.com/nf-core/ampliseq/pull/795) - Template update for nf-core/tools version 3.0.2
 - [#786](https://github.com/nf-core/ampliseq/pull/786) - Creation of the summary report was failing with `--dada_ref_taxonomy silva=132`
 - [#792](https://github.com/nf-core/ampliseq/pull/792) - Remove white spaces in process tags to avoid errors on some systems
 

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/2.12.0" 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/2.12.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-ampliseq-methods-description":
     order: -1000

docs/usage.md

@@ -323,7 +323,7 @@ nextflow pull nf-core/ampliseq
 
 It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
-First, go to the [nf-core/ampliseq releases page](https://github.com/nf-core/ampliseq/releases) and find the latest pipeline version - numeric only (eg. `2.4.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.4.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
+First, go to the [nf-core/ampliseq releases page](https://github.com/nf-core/ampliseq/releases) and find the latest pipeline version - numeric only (eg. `2.12.0`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 2.12.0`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
 

nextflow.config

@@ -286,7 +286,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 
 // Load nf-core/ampliseq custom profiles from different institutions.
 // nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/ampliseq.config" : "/dev/null"
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/ampliseq.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -346,7 +346,7 @@ manifest {
     description     = """Amplicon sequencing analysis workflow using DADA2 and QIIME2"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '2.12.0dev'
+    version         = '2.12.0'
     doi             = '10.5281/zenodo.1493841,10.3389/fmicb.2020.550420'
 }