From c54a846c72b1239b26838110477619eea75cd1b2 Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Tue, 15 Oct 2019 10:14:11 -0500
Subject: [PATCH] Added container functionality
---
workflow/conf/biohpc.config | 23 +++++++++++++++++++----
workflow/rna-seq.nf | 4 ++--
2 files changed, 21 insertions(+), 6 deletions(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 0ea7440..6bd7db1 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -1,10 +1,10 @@
process {
executor = 'slurm'
- queue='super'
+ queue = 'super'
// Process specific configuration
- withLabel:getData {
- executor = 'super'
+ withName:getData {
+ container = 'docker://bicf/bdbag:1.0'
}
}
@@ -28,4 +28,19 @@ report {
tower {
accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
enabled = true
-}
\ No newline at end of file
+}
+
+singularity {
+ enabled = true
+ cacheDir = '/project/BICF/BICF_Core/s181706/github/gudmap/rna-seq/workflow/singularity'
+}
+
+env {
+ http_proxy = "http://proxy.swmed.edu:3128"
+ https_proxy = "http://proxy.swmed.edu:3128"
+ HTTP_PROXY = "http://proxy.swmed.edu:3128"
+ HTTPS_PROXY = "http://proxy.swmed.edu:3128"
+ all_proxy = "http://proxy.swmed.edu:3128"
+ ALL_PROXY = "http://proxy.swmed.edu:3128"
+}
+
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d839044..86e537b 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -19,7 +19,7 @@ outDir = params.outDir
*/
process getData {
publishDir "${outDir}/temp/getData", mode: "symlink"
- conda "${baseDir}/conf/conda.env.bdbag.yml"
+// conda "${baseDir}/conf/conda.env.bdbag.yml"
input:
file bdbag
@@ -46,4 +46,4 @@ outDir = params.outDir
sh ${baseDir}/scripts/renameFastq.sh \${study}
echo LOG: fastq.gz files renamed to replicate RID
"""
- }
\ No newline at end of file
+ }
--
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