From 4559382903042041ad650aaae2468e5386ec56b4 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 9 Sep 2020 20:54:26 -0500
Subject: [PATCH] Add param for ref source
---
workflow/conf/aws.config | 4 ++++
workflow/conf/biohpc.config | 4 ++++
workflow/rna-seq.nf | 10 ++++++++--
3 files changed, 16 insertions(+), 2 deletions(-)
diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config
index b5054f7..c26e1a4 100644
--- a/workflow/conf/aws.config
+++ b/workflow/conf/aws.config
@@ -1,3 +1,7 @@
+params {
+ refSource = "aws"
+}
+
workDir = 's3://gudmap-rbk.output/work'
aws.client.storageEncryption = 'AES256'
aws {
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index efe86be..d2a933f 100755
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -1,3 +1,7 @@
+params {
+ refSource = "biohpc
+}
+
process {
executor = 'slurm'
queue = 'super'
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d5c86e2..b12b1f1 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -20,6 +20,7 @@ params.refERCCVersion = "92"
params.outDir = "${baseDir}/../output"
// Define override input variable
+params.refSource = "biohpc"
params.inputBagForce = ""
params.fastqsForce = ""
params.speciesForce = ""
@@ -50,8 +51,13 @@ if (params.source == "dev") {
} else if (params.source == "production") {
source = "www.gudmap.org"
}
-referenceBase = "s3://bicf-references"
-//referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references"
+if (params.refSource == "biohpc") {
+ referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references"
+} else if (params.refSource == "aws") {
+ referenceBase = "s3://bicf-references"
+} else if (params.refSource == "datahub") {
+ referenceBase = "dev.gudmap.org"
+}
referenceInfer = Channel.fromList(["ERCC","GRCh","GRCm"])
multiqcConfig = Channel.fromPath("${baseDir}/conf/multiqc_config.yaml")
bicfLogo = Channel.fromPath("${baseDir}/../docs/bicf_logo.png")
--
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