updated config to pass linting

.nf-core.yml

@@ -1,5 +1,5 @@
 repository_type: pipeline
-nf_core_version: "3.0.1"
+nf_core_version: "3.0.2"
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md

nextflow.config

@@ -1029,21 +1029,26 @@ params {
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
+
+/*
+
+Below options require additional parametrs to be added.
+
+config_profile_name        = null
+config_profile_description = null
+
+custom_config_version      = 'master'
+custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+config_profile_contact     = null
+config_profile_url         = null
+
 // Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
-// Load mk-kondo/mikrokondo custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/mikrokondo.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/mikrokondo profiles: ${params.custom_config_base}/pipeline/mikrokondo.config")
-// }
+// Load nf-core/viralrecon custom profiles from different institutions.
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/mikrokondo.config" : "/dev/null"
 
+*/
 
 profiles {
     debug {
@@ -1141,7 +1146,7 @@ process.ext.override_configured_container_registry = true
 plugins {
     //id '[email protected]'
     id '[email protected]'
-    id 'nf-prov'
+    id 'nf-prov@1.2.4'
     id '[email protected]'
 }