From 17962772abdb8d1bc7633f0299aa1eeeb63de7e8 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 15:44:55 -0600
Subject: [PATCH] Update replicate bdbag export config name
---
.gitlab-ci.yml | 2 +-
...eplicate_export_config.json => Replicate_For_Input_Bag.json} | 0
workflow/rna-seq.nf | 2 +-
3 files changed, 2 insertions(+), 2 deletions(-)
rename workflow/conf/{replicate_export_config.json => Replicate_For_Input_Bag.json} (100%)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9f94a7d..8ae1b79 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -26,7 +26,7 @@ getBag:
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
- singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-download-cli --version > version_deriva.txt
- - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=Q-Y5F6
+ - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
- pytest -m getBag
artifacts:
name: "$CI_JOB_NAME"
diff --git a/workflow/conf/replicate_export_config.json b/workflow/conf/Replicate_For_Input_Bag.json
similarity index 100%
rename from workflow/conf/replicate_export_config.json
rename to workflow/conf/Replicate_For_Input_Bag.json
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 540d5be..25f4a24 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -59,7 +59,7 @@ speciesForce = params.speciesForce
email = params.email
// Define fixed files
-replicateExportConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
+replicateExportConfig = Channel.fromPath("${baseDir}/conf/Replicate_For_Input_Bag.json")
executionRunExportConfig = Channel.fromPath("${baseDir}/conf/Execution_Run_For_Output_Bag.json")
if (params.source == "dev") {
source = "dev.gudmap.org"
--
GitLab