Implement feature skipping and add versioning

.nf-core.yml

@@ -1,2 +1,19 @@
+bump_version: null
+lint: null
+nf_core_version: 3.0.2
+org_path: null
 repository_type: pipeline
-nf_core_version: "2.14.1"
+template:
+  author: Nico Trummer
+  description: A single cell transcriptomics pipeline for QC, integration and making
+    the results presentable
+  force: false
+  is_nfcore: true
+  name: scdownstream
+  org: nf-core
+  outdir: .
+  skip_features:
+    - fastqc
+    - igenomes
+  version: 0.0.1dev
+update: null

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).
 
-## v1.0dev - [date]
+## v0.0.1dev - [2024-10-17]
 
 Initial release of nf-core/scdownstream, created with the [nf-core](https://nf-co.re/) template.
 

nextflow.config

@@ -263,7 +263,7 @@ manifest {
     description     = """A single cell transcriptomics pipeline for QC, integration and making the results presentable"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0dev'
+    version         = '0.0.1dev'
     doi             = ''
 }