From 53c180863333d6fc0422475ede758a62e5d9568a Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 19 Feb 2021 18:11:58 -0600
Subject: [PATCH] Update file refs in .nf to match new locations
---
rna-seq.nf | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 59f2039..30fb31a 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -9,8 +9,8 @@
// ######## #### ###### ##
// Define input variables
-params.deriva = "${baseDir}/../test_data/auth/credential.json"
-params.bdbag = "${baseDir}/../test_data/auth/cookies.txt"
+params.deriva = "${baseDir}/test_data/auth/credential.json"
+params.bdbag = "${baseDir}/test_data/auth/cookies.txt"
//params.repRID = "16-1ZX4"
params.repRID = "Q-Y5F6"
params.source = "dev"
@@ -72,9 +72,9 @@ spikeForce = params.spikeForce
email = params.email
// Define fixed files and variables
-bdbagConfig = Channel.fromPath("${baseDir}/conf/bdbag.json")
-replicateExportConfig = Channel.fromPath("${baseDir}/conf/Replicate_For_Input_Bag.json")
-executionRunExportConfig = Channel.fromPath("${baseDir}/conf/Execution_Run_For_Output_Bag.json")
+bdbagConfig = Channel.fromPath("${baseDir}/workflow/conf/bdbag.json")
+replicateExportConfig = Channel.fromPath("${baseDir}/workflow/conf/Replicate_For_Input_Bag.json")
+executionRunExportConfig = Channel.fromPath("${baseDir}/workflow/conf/Execution_Run_For_Output_Bag.json")
if (params.source == "dev") {
source = "dev.gudmap.org"
} else if (params.source == "staging") {
@@ -88,7 +88,7 @@ if (params.refSource == "biohpc") {
referenceBase = "www.gudmap.org"
}
referenceInfer = Channel.fromList(["ERCC","GRCh","GRCm"])
-multiqcConfig = Channel.fromPath("${baseDir}/conf/multiqc_config.yaml")
+multiqcConfig = Channel.fromPath("${baseDir}/workflow/conf/multiqc_config.yaml")
bicfLogo = Channel.fromPath("${baseDir}/docs/bicf_logo.png")
softwareReferences = Channel.fromPath("${baseDir}/docs/software_references_mqc.yaml")
softwareVersions = Channel.fromPath("${baseDir}/docs/software_versions_mqc.yaml")
--
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