From b7cbd6a74ccca3b76a3f00884009d7a853e26437 Mon Sep 17 00:00:00 2001
From: Robert Literman <jazz710@gmail.com>
Date: Wed, 22 Jan 2025 13:57:24 -0500
Subject: [PATCH] Do not enable conda by default

---
 conf/profiles.config | 21 +++++++++++----------
 nextflow.config      |  5 +----
 2 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/conf/profiles.config b/conf/profiles.config
index b8db2dd..853e7e4 100644
--- a/conf/profiles.config
+++ b/conf/profiles.config
@@ -20,18 +20,14 @@ profiles {
         params.mash_module = "/nfs/software/modules/mash/2.3"
         params.trim_name = "_contigs_skesa"
     }
-    csp2_galaxy {
+    csp2_reedling {
         conda.enabled = true
         conda.useMicromamba = true
         conda.cacheDir = "${projectDir}/CSP2_env"
-        process.conda = "${projectDir}/conf/CSP2.yaml"
-        
-        process.queue = "ondemand-small"
-
-        executor.$slurm.exitReadTimeout = 120000
+        process.conda = "${projectDir}/conf/CSP2.yaml"        
 
         process.executor = 'slurm'
-        params.cores = 1
+        params.cores = 48
         params.python_module = ""
         params.mummer_module = ""
         params.skesa_module = ""
@@ -40,14 +36,18 @@ profiles {
         params.mash_module = ""
         params.trim_name = ""
     }
-    csp2_reedling {
+    csp2_galaxy {
         conda.enabled = true
         conda.useMicromamba = true
         conda.cacheDir = "${projectDir}/CSP2_env"
-        process.conda = "${projectDir}/conf/CSP2.yaml"        
+        process.conda = "${projectDir}/conf/CSP2.yaml"
+        
+        process.queue = "ondemand-small"
+
+        executor.$slurm.exitReadTimeout = 120000
 
         process.executor = 'slurm'
-        params.cores = 48
+        params.cores = 1
         params.python_module = ""
         params.mummer_module = ""
         params.skesa_module = ""
@@ -56,4 +56,5 @@ profiles {
         params.mash_module = ""
         params.trim_name = ""
     }
+
 }
diff --git a/nextflow.config b/nextflow.config
index 76f973a..6e7425f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -6,13 +6,10 @@
 ----------------------------------------------------------------------------------------
 */
 
-// Enable conda
-conda.enabled = true
-
 // Import profile settings
 includeConfig "conf/profiles.config"
 
-// CPU/memory settings
+// CPU/memory settings (Required for Galaxy)
 process {
     withLabel: 'mummerMem' {
         task_name = 'CSP2-MUMmer'