From b9d9c5866d3630d535fd3d863a034ed1555f2bd1 Mon Sep 17 00:00:00 2001
From: Harshil Patel <patelh@localhost.localdomain>
Date: Sat, 24 Nov 2018 10:43:17 +0000
Subject: [PATCH] Moved custom Institutional configs to nf-core configs on
 github

---
 CHANGELOG.md                                  |  8 ++++
 .../nextflow.config                           | 42 +++++++------------
 2 files changed, 23 insertions(+), 27 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 17b65d5018..bb4194c289 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # nf-core/tools: Changelog
 
+## v1.3dev
+* Institutional custom config profiles moved to github `nf-core/configs`
+    * These will now be maintained centrally as opposed to being shipped with the pipelines in `conf/`
+    * Load `base.config` by default for all profiles
+    * Removed profiles named `standard` and `none`
+    * Added parameter `--igenomesIgnore` so `igenomes.config` isnt loaded if parameter clashes are observed
+    * Added parameter `--custom_config_version` for custom config version control. Can use this parameter to provide commit id for reproducibility. Defaults to `master`  
+
 ##[v1.3](https://github.com/nf-core/tools/releases/tag/1.3) - 2018-11-21
 * `nf-core create` command line interface updated
     * Interactive prompts for required arguments if not given
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
index ac3bdf090e..0fbaa34ec5 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -32,46 +32,34 @@ params {
   clusterOptions = false
   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/${params.custom_config_version}/nfcore_custom.config"
+
 profiles {
-  awsbatch {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/awsbatch.config'
-    includeConfig 'conf/igenomes.config'
-  }
-  binac {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/binac.config'
-  }
-  cfc {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/cfc.config'
-  } 
+  awsbatch { includeConfig 'conf/awsbatch.config' }
   conda { process.conda = "$baseDir/environment.yml" }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   docker {
     docker.enabled = true
     process.container = params.container
   }
-  none {
-    // Don't load any config (for use with custom home configs)
-  }
   singularity {
     singularity.enabled = true
     process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
   }
-  standard {
-    includeConfig 'conf/base.config'
-  }
-  test {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/test.config'
-  }
-  uzh {
-    includeConfig 'conf/base.config'
-    includeConfig 'conf/uzh.config'
-  }
+  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