From 38f026a18c9430dadb6d7ceb5627b91fd718e980 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 4 Oct 2017 15:16:36 -0500
Subject: [PATCH] Add in nextflow config for loading modules.
---
nextflow.config | 5 -----
workflow/conf/biohpc.conf | 13 +++++++++++++
workflow/nextflow.config | 5 +++++
3 files changed, 18 insertions(+), 5 deletions(-)
delete mode 100644 nextflow.config
create mode 100644 workflow/conf/biohpc.conf
create mode 100644 workflow/nextflow.config
diff --git a/nextflow.config b/nextflow.config
deleted file mode 100644
index 7fc857a..0000000
--- a/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process.executor='slurm'
-process.queue='super'
-process.time='5d'
-
-
diff --git a/workflow/conf/biohpc.conf b/workflow/conf/biohpc.conf
new file mode 100644
index 0000000..3587d62
--- /dev/null
+++ b/workflow/conf/biohpc.conf
@@ -0,0 +1,13 @@
+process {
+ executor = 'slurm'
+ queue='super'
+
+ // Process specific configuration
+ $checkDesignFile {
+ module = ['python/3.6.1-2-anaconda']
+ }
+ $trim_galore {
+ module = ['python/3.6.1-2-anaconda', 'trimgalore/0.4.1']
+ cpus = 32
+ }
+}
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
new file mode 100644
index 0000000..30e47ea
--- /dev/null
+++ b/workflow/nextflow.config
@@ -0,0 +1,5 @@
+profiles {
+ standard {
+ includeConfig 'conf/biohpc.config'
+ }
+}
--
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