Remove old configs

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * [#111](https://github.com/nf-core/eager/pull/110) - Allow [Zipped FastA reference input](https://github.com/nf-core/eager/issues/91)
 * [#113](https://github.com/nf-core/eager/pull/113) - All files are now staged via channels, which is considered best practice by Nextflow. 
 * [#114](https://github.com/nf-core/eager/pull/113) - Add proper runtime defaults for multiple processes 
+* [#118](https://github.com/nf-core/eager/pull/118) - Add centralized configs handling
 
 ### `Fixed`
 * [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107)

nextflow.config

@@ -31,56 +31,35 @@ params {
   // AWS Batch
   awsqueue = false
   awsregion = 'eu-west-1'
+
+  igenomesIgnore = false
+  custom_config_version = 'master'
 }
 
+// Load base.config by default for all pipelines
+includeConfig 'conf/base.config'
+
+// Load nf-core custom profiles from different Institutions
+includeConfig "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/nfcore_custom.config"
+
 profiles {
+  awsbatch { includeConfig 'conf/awsbatch.config' }
   conda { process.conda = "$baseDir/environment.yml" }
+  debug { process.beforeScript = 'echo $HOSTNAME' }
   docker {
     docker.enabled = true
     process.container = params.container
   }
   singularity {
     singularity.enabled = true
+    process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
   }
-  standard {
-    includeConfig 'conf/base.config'
-  }
-  awsbatch {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/awsbatch.config'
-    includeConfig 'conf/igenomes.config'
-  }
-  binac {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/binac.config'
-  }
-  uzh {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/uzh.config'
-  }
-  phoenix {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/acad-pheonix.config'
-  }
-  shh {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/shh.config'
-  }
-  cfc {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/cfc.config'
-  }
-  standard {
-    includeConfig 'conf/base.config'
-  }
-  test {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/test.config'
-  }
-  debug { process.beforeScript = 'echo $HOSTNAME' }
-  none {
-    // Don't load any config (for use with custom home configs)
-  }
+  test { includeConfig 'conf/test.config' }
+}
+
+// Load igenomes.config if required
+if(!params.igenomesIgnore){
+  includeConfig 'conf/igenomes.config'
 }
 
 // Capture exit codes from upstream processes when piping