prepare release 3.1.1

.github/RELEASE_CHECKLIST.md

@@ -12,6 +12,8 @@
 4. Sync `dev` and checkout a new branch for the release
 5. Bump version:
    - `nf-core bump-version . <VERSION>`
+   - edit `docs/images/sarek_indices_subway.svg`
+   - generate a new `docs/images/sarek_indices_subway.png`
    - edit `docs/images/sarek_subway.svg`
    - generate a new `docs/images/sarek_subway.png`
    - edit `docs/images/sarek_workflow.svg`
@@ -28,6 +30,8 @@
     - `git checkout upstream/master -- CHANGELOG.md`
 14. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version
 15. Checkout figures from `master`
+    - `git checkout upstream/master -- docs/images/sarek_indices_subway.svg`
+    - `git checkout upstream/master -- docs/images/sarek_indices_subway.png`
     - `git checkout upstream/master -- docs/images/sarek_subway.svg`
     - `git checkout upstream/master -- docs/images/sarek_subway.png`
     - `git checkout upstream/master -- docs/images/sarek_workflow.svg`

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).
 
-## [dev]
+## [3.1.1](https://github.com/nf-core/sarek/releases/tag/3.1.1) - Lilla Luleälven
+
+Lilla Luleälven river's main affluent is Rapaätno.
 
 ### Added
 
@@ -14,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [#855](https://github.com/nf-core/sarek/pull/855) - Speed up duplicate marking by using `samtools` for CRAM conversion
+- [#858](https://github.com/nf-core/sarek/pull/858) - Prepare release `3.1.1`
 
 ### Fixed
 

nextflow.config

@@ -280,7 +280,7 @@ manifest {
     description     = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version = '3.2dev'
+    version = '3.1.1'
     doi             = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683'
 }