From bdb02167d4ba64a6f8378d03c596834ff510d9f3 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 21:49:54 -0600
Subject: [PATCH] Use updated input bag name
---
.gitlab-ci.yml | 2 +-
workflow/rna-seq.nf | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b63a579..0e24cc0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -50,7 +50,7 @@ getData:
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- unzip ./test_data/bag/staging/Q-Y5F6_inputBag_20201228.zip
- - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag_20201228 Q-Y5F6 TEST
+ - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag Q-Y5F6 TEST
- pytest -m getData
artifacts:
name: "$CI_JOB_NAME"
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 30f9bd1..00b8c96 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -241,7 +241,7 @@ process getData {
# bag fetch fastq's only and rename by repRID
echo -e "LOG: fetching replicate bdbag" >> ${repRID}.getData.log
- sh ${script_bdbagFetch} \${replicate} ${repRID}
+ sh ${script_bdbagFetch} \${replicate::-9} ${repRID}
echo -e "LOG: fetched" >> ${repRID}.getData.log
"""
}
--
GitLab