Merge pull request #111 from drpatelh/master

Update awsbatch.config

conf/awsbatch.config

@@ -1,14 +1,16 @@
-//Nextflow config file for running on AWS batch
-
-params {
-  awsqueue = false
-  awsregion = 'eu-west-1'
-  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
-  config_profile_description = 'AWSBATCH Cloud Profile'
-  config_profile_name = 'AWSBATCH'
-  config_profile_url = 'https://aws.amazon.com/batch/'
-  tracedir = './'
-}
-
-process.executor = 'awsbatch'
-executor.awscli = '/home/ec2-user/miniconda/bin/aws'
+//Nextflow config file for running on AWS batch
+params {
+  config_profile_description = 'AWSBATCH Cloud Profile'
+  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
+  config_profile_url = 'https://aws.amazon.com/batch/'
+
+  awsqueue = false
+  awsregion = 'eu-west-1'
+  awscli = '/home/ec2-user/miniconda/bin/aws'
+  tracedir = './'
+}
+
+process.executor = 'awsbatch'
+process.queue = params.awsqueue
+aws.region = params.awsregion
+executor.awscli = params.awscli

docs/awsbatch.md

@@ -1,4 +1,4 @@
 # nf-core/configs: awsbatch Configuration
 
 To be used with `awsbatch`.
-Custom queue and region can be entered with `params.awsqueue` and `params.region` respectively.
+Custom queue, region and CLI path can be supplied with `params.awsqueue`, `params.awsregion`, `params.awscli`, respectively.