From 65c566856889b3d49fc2fd21a9728be1f9c0286d Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Thu, 12 Dec 2019 13:02:44 +0000
Subject: [PATCH 1/3] Update config

---
 conf/awsbatch.config | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/conf/awsbatch.config b/conf/awsbatch.config
index 18c8600..63e0dab 100644
--- a/conf/awsbatch.config
+++ b/conf/awsbatch.config
@@ -1,14 +1,14 @@
 //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/'
+  config_profile_contact = 'Alexander Peltzer (@apeltzer)'
+  config_profile_url = 'https://aws.amazon.com/de/batch/'
+
   tracedir = './'
 }
 
 process.executor = 'awsbatch'
-executor.awscli = '/home/ec2-user/miniconda/bin/aws'
+process.queue = params.awsqueue
+aws.region = params.awsregion
+executor.awscli = params.awscli

From 0779d25255bb32f1e51fdc0d4ff858e3d6fb6c8c Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Thu, 12 Dec 2019 13:02:51 +0000
Subject: [PATCH 2/3] Update docs

---
 docs/awsbatch.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/awsbatch.md b/docs/awsbatch.md
index 94eb7ec..c00acef 100644
--- a/docs/awsbatch.md
+++ b/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.

From 089b5b8e3bbab55484e41d0e5a450d7233d874e9 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Thu, 12 Dec 2019 13:44:37 +0000
Subject: [PATCH 3/3] Update config

---
 conf/awsbatch.config | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/conf/awsbatch.config b/conf/awsbatch.config
index 63e0dab..2e5f83c 100644
--- a/conf/awsbatch.config
+++ b/conf/awsbatch.config
@@ -1,14 +1,16 @@
-//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/de/batch/'
-
-  tracedir = './'
-}
-
-process.executor = 'awsbatch'
-process.queue = params.awsqueue
-aws.region = params.awsregion
-executor.awscli = params.awscli
+//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