Revert nf-cmgg/configs back to nf-core/configs

CHANGELOG.md

@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## v1.0.3
 
 - Fixed an issue where pool grouping for multiqc wasn't properly performed on pipeline resume
+- Revert the default configs base to the nf-core configs in preparation of converting nf-cmgg/configs to a private repo
 
 ## v1.0.2
 

main.nf

@@ -29,7 +29,7 @@ params {
     input: Path
 
     // The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
-    outdir: Path
+    outdir: String
 
     // Email address for completion summary.
     email: String?

nextflow.config

@@ -20,8 +20,8 @@ params {
     config_profile_name        = null
     config_profile_description = null
 
-    custom_config_version        = 'main'
-    custom_config_base           = "https://raw.githubusercontent.com/nf-cmgg/configs/${params.custom_config_version}"
+    custom_config_version        = 'master'
+    custom_config_base           = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
 

workflows/sampletracking.nf

@@ -258,7 +258,7 @@ workflow SAMPLETRACKING {
     softwareVersionsToYAML(topic_versions.versions_file)
         .mix(topic_versions_string)
         .collectFile(
-            storeDir: "${outdir.toUriString()}/pipeline_info",
+            storeDir: "${outdir}/pipeline_info",
             name: 'nf_cmgg_sampletracking_software_mqc_versions.yml',
             sort: true,
             newLine: true,