diff --git a/CHANGELOG.md b/CHANGELOG.md
index 943350247..ab5bdbc53 100644
--- a/CHANGELOG.md
+++ b/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)
diff --git a/conf/acad-pheonix.config b/conf/acad-pheonix.config
deleted file mode 100644
index ee00208b5..000000000
--- a/conf/acad-pheonix.config
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * ----------------------------------------------------------------------------
- *  Nextflow config file for use with Singularity on Phoenix Cluster Adelaide
- * ----------------------------------------------------------------------------
- * Defines basic usage limits and singularity image id.
- */
-
-singularity {
-    enabled = true
-    autoMounts = true
-}
-
-process {
-    beforeScript = 'module load Singularity/2.5.2-GCC-5.4.0-2.26'
-    executor = 'slurm'
-}
-
-params {
-  max_memory = 128.GB
-  max_cpus = 32
-  max_time = 48.h
-}
diff --git a/conf/binac.config b/conf/binac.config
deleted file mode 100644
index 68ba98f1e..000000000
--- a/conf/binac.config
+++ /dev/null
@@ -1,22 +0,0 @@
-/*
- * ----------------------------------------------------------------------------
- *  Nextflow config file for use with Singularity on BINAC cluster in Tuebingen
- * ----------------------------------------------------------------------------
- * Defines basic usage limits and singularity image id.
- */
-
-singularity {
-    enabled = true
-}
-
-process {
-    beforeScript = 'module load devel/singularity/2.6.0'
-    executor = 'pbs'
-    queue = 'short'
-}
-
-params {
-  max_memory = 128.GB
-  max_cpus = 28
-  max_time = 48.h
-}
diff --git a/conf/cfc.config b/conf/cfc.config
deleted file mode 100644
index 7915e9714..000000000
--- a/conf/cfc.config
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * -------------------------------------------------------------
- *  Nextflow config file for use with Singularity on CFC at QBIC
- * -------------------------------------------------------------
- * Defines basic usage limits and singularity image id.
- */
-
-singularity {
-    enabled = true
-}
-
-/*
-*To be improved by process specific configuration asap, once our CFC cluster has the extra options removed - till then, task.attempt in NextFlow is not supported there.
-*/
-
-process {
-    beforeScript = 'module load qbic/singularity_slurm/2.5.1'
-    executor = 'slurm'
-}
-
-params {
-  max_memory = 60.GB
-  max_cpus = 24
-  max_time = 140.h
-}
diff --git a/conf/shh.config b/conf/shh.config
deleted file mode 100644
index a402e5dca..000000000
--- a/conf/shh.config
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * -------------------------------------------------------------
- *  Nextflow config file for use with Singularity at SHH Clusters
- * -------------------------------------------------------------
- * Defines basic usage limits and singularity image id.
- */
-
-singularity {
-    enabled = true
-    cacheDir = "/projects1/users/$USER/nextflow/nf_cache/singularity/"
-}
-
-/*
-* To be improved by process specific resource requests
-* By default, take the medium queue, smaller processes might just go to short (e.g. multiqc or similar things)
-*/
-
-process {
-    executor = 'slurm'
-    queue = 'medium'
-
-    
-    withName:makeFastaIndex {
-        queue = 'short'
-        time = 2.h
-    }
-    withName:makeSeqDict {
-        queue = 'short'
-        time = 2.h
-    }
-}
-
-
-params {
-  max_memory = 734.GB
-  max_cpus = 64
-  max_time = 48.h
-}
diff --git a/conf/uzh.config b/conf/uzh.config
deleted file mode 100644
index 0a3fac65f..000000000
--- a/conf/uzh.config
+++ /dev/null
@@ -1,19 +0,0 @@
-/*
- * --------------------------------------------------------------------------------
- *  Nextflow config file for use with Singularity on University of Zurich Cluster
- * --------------------------------------------------------------------------------
- */
-
-singularity {
-    enabled = true
-}
-
-process {
-    executor = 'slurm'
-}
-
-params {
-  max_memory = 1800.GB
-  max_cpus = 112
-  max_time = 168.h
-}
diff --git a/nextflow.config b/nextflow.config
index a2f836d5c..012e32934 100644
--- a/nextflow.config
+++ b/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