diff --git a/.nf-core.yml b/.nf-core.yml
index 6ec4fc101f..2bc4a45cc1 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -2,10 +2,7 @@ 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
@@ -13,3 +10,4 @@ lint:
- lib/NfcoreSchema.groovy
schema_params: False
template_strings: False
+ multiqc_config: False
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2e354ddc58..3a4222039a 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index aabf286ce8..6a75b8ce7e 100644
--- a/assets/multiqc_config.yml
+++ b/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 nf-core/sarek
+ This report has been generated by the nf-core/sarek
analysis pipeline. For information about how to interpret these results, please see the
- documentation.
+ documentation.
report_section_order:
"nf-core-sarek-methods-description":
order: -1000
diff --git a/nextflow.config b/nextflow.config
index 7996605605..062787ad85 100644
--- a/nextflow.config
+++ b/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'
}