From a70eaaf3239f23cfa590f1521a820670e24e1bbd Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 27 Apr 2019 14:48:44 -0500
Subject: [PATCH] Force mkdir and ln in CI

---
 .gitlab-ci.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f3b389f..f205b10 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,11 +3,11 @@ before_script:
   - module load python/3.6.1-2-anaconda
   - module load nextflow/0.31.1_Ignite
   - mkdir test_data/hu.v2s1r500
-  - mkdir test_data/mu.v2s2r10k
-  - mkdir test_data/hu.v3s2r10k
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
+  - mkdir -p test_data/mu.v2s2r10k
+  - mkdir -p test_data/hu.v3s2r10k
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s1r500/* test_data/hu.v2s1r500/
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v2s2r10k/* test_data/mu.v2s2r10k/
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
 
 stages:
   - astrocyte
-- 
GitLab