Merge pull request nf-core#1198 from maxulysse/prepare_release_3_3

CHORES: Prepare 3.3

.nf-core.yml

@@ -2,14 +2,12 @@ repository_type: pipeline
 lint:
   files_exist:
     - conf/modules.config
-    - conf/test.config
-    - conf/test_full.config
   files_unchanged:
-    - assets/multiqc_config.yml
     - assets/nf-core-sarek_logo_light.png
     - docs/images/nf-core-sarek_logo_dark.png
     - docs/images/nf-core-sarek_logo_light.png
     - lib/NfcoreTemplate.groovy
     - lib/NfcoreSchema.groovy
   schema_params: False
   template_strings: False
+  multiqc_config: False

CHANGELOG.md

@@ -5,7 +5,9 @@ All notable changes to this project will be documented in this file.
 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).
 
-## 3.3dev
+## [3.3.0](https://github.com/nf-core/sarek/releases/tag/3.3.0) - Rapaselet
+
+Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe massif (formerly written Piellorieppe) and the Skårki massif.
 
 ### Added
 
@@ -30,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1174](https://github.com/nf-core/sarek/pull/1174) - Updating multiqc to v1.15
 - [#1179](https://github.com/nf-core/sarek/pull/1179) - Unhide params `trim_fastq`, `umi_read_structure`, and `aligner`
 - [#1180](https://github.com/nf-core/sarek/pull/1180) - Updating the nf-core modules
+- [#1198](https://github.com/nf-core/sarek/pull/1198) - Prepare release `3.3.0`
 
 ### Fixed
 

assets/multiqc_config.yml

@@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/sarek/
 custom_logo_title: "nf-core/sarek"
 
 report_comment: >
-  This report has been generated by the <a href="/nf-core/sarek/3.3dev" target="_blank">nf-core/sarek</a>
+  This report has been generated by the <a href="/nf-core/sarek/releases/tag/3.3.0" target="_blank">nf-core/sarek</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/sarek/3.3dev/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/sarek/3.3.0/docs/output/" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-sarek-methods-description":
     order: -1000

nextflow.config

@@ -311,13 +311,6 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
-// Set default registry for Docker, Singularity and Podman independent of -profile
-// Will not be used unless Docker, Singularity and Podman are enabled
-// Set to your registry if you have a mirror of containers
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
-
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true
@@ -343,7 +336,7 @@ manifest {
     description     = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.3dev'
+    version         = '3.3.0'
     doi             = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683'
 }