From a36c189e2748cc65b4e6cdc8b70e99a3c1bd2429 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 11 May 2020 09:59:00 -0500
Subject: [PATCH] Add source param for getBag #50
---
workflow/rna-seq.nf | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index de8bf96..8b6166a 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -13,6 +13,7 @@ params.deriva = "${baseDir}/../test_data/auth/credential.json"
params.bdbag = "${baseDir}/../test_data/auth/cookies.txt"
//params.repRID = "16-1ZX4"
params.repRID = "Q-Y5JA"
+params.source = "dev"
params.refMoVersion = "38.p6.vM22"
params.refHuVersion = "38.p12.v31"
params.refERCCVersion = "92"
@@ -34,6 +35,13 @@ logsDir = "${outDir}/Logs"
// Define fixed files
derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
+if (params.source == "dev") {
+ source = "dev.gudmap.org"
+} else if (params.source == "staging") {
+ source = "staging.gudmap.org"
+} else if (params.source == "production") {
+ source = "www.gudmap.org"
+}
//referenceBase = "s3://bicf-references"
referenceBase = "/project/BICF/BICF_Core/shared/gudmap/references"
referenceInfer = Channel.fromList(["ERCC","GRCh","GRCm"])
@@ -100,7 +108,7 @@ process getBag {
# deriva-download replicate RID
echo -e "LOG: fetching bagit for ${repRID} in GUDMAP" >> ${repRID}.getBag.log
- deriva-download-cli staging.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID}
+ deriva-download-cli ${source} --catalog 2 ${derivaConfig} . rid=${repRID}
echo -e "LOG: fetched" >> ${repRID}.getBag.log
"""
}
--
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