From bfad4229168224318a6484012af8bddf93bc99ba Mon Sep 17 00:00:00 2001
From: Caspar Gross <mail@caspar.one>
Date: Sun, 28 Apr 2019 15:55:24 +0200
Subject: [PATCH] type in config params

---
 nextflow.config | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 6559c5d..4f2d71c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -13,29 +13,43 @@ manifest {
     description = 'Hybrid assembly pipeline using long and short reads'
     name = 'HybridAssembly'
     nextflowVersion = '>=0.32.0'
-    version = '0.5'
+    version = '1.0'
 }
 
+// Default parameters used in all profiles
+params { 
+    help = false
+    version = false
+    
+    targetShortReadCov = 100
+    targetLongReadCov = 100
+    minContigLenth = 50
+
+    py27 = "source activate ha_py27" // Assume conda is already in path
+    py36 = "source activate ha_py36" // Assume conda is already in path
+}
+
+
 profiles 
     {
     standard {
         includeConfig 'conf/base.config'
- //       includeConfig 'conf/docker.config'
+        includeConfig 'conf/docker.config'
     }
     app {
         includeConfig 'conf/app.config'
-//        includeConfig 'conf/docker.config'
+        includeConfig 'conf/docker.config'
     }
     local {
         includeConfig 'conf/base.config'
     }   
     test {
         includeConfig 'conf/test.config'
-//        includeConfig 'conf/docker.config'
+        includeConfig 'conf/docker.config'
     }
     testlr {
         includeConfig 'conf/testlr.config'
-//        includeConfig 'conf/docker.config'
+        includeConfig 'conf/docker.config'
     }
     testsingularity {
         includeConfig 'conf/test.config'