Merge pull request #415 from jfy133/tsv-input

Re-add accidently removed nf-core config profile loading

nextflow.config

@@ -209,7 +209,7 @@ params {
   awsregion = 'eu-west-1'
   igenomes_ignore = false
   custom_config_version = 'master'
-  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/"
+  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
   hostnames = false
   config_profile_description = false
   config_profile_contact = false
@@ -229,7 +229,14 @@ process.container = 'nfcore/eager:dev'
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-// Load nf-core/eager custom profiles from different Institutions
+// 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: ${params.custom_config_base}/nfcore_custom.config")
+}
+
+// Load nf-core/eager custom profiles from different institutions
 try {
   includeConfig "${params.custom_config_base}/pipeline/eager.config"
 } catch (Exception e) {
@@ -256,7 +263,6 @@ profiles {
 
 
 profiles {
-  awsbatch { includeConfig 'conf/awsbatch.config'}
   conda { process.conda = "$baseDir/environment.yml"}
   debug { process.beforeScript = 'echo $HOSTNAME'}
   docker {