From f52363f61715aa06ced59532d5e3cb3355fd239e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 1 Sep 2018 11:43:55 -0500
Subject: [PATCH] Fix ci.yml

---
 .gitignore           | 3 ++-
 .gitlab-ci.yml       | 2 +-
 test_data/design.csv | 4 ++++
 3 files changed, 7 insertions(+), 2 deletions(-)
 create mode 100755 test_data/design.csv

diff --git a/.gitignore b/.gitignore
index 350e9da..b74cce0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -99,7 +99,8 @@ ENV/
 .mypy_cache/
 
 # nextflow analysis folders/files
-/test_data/*
+/test_data/*.fastq.gz
+/test_data/*.fastq
 /workflow/.nextflow/*
 /workflow/work/*
 /workflow/output/*
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b44881a..08bb4e9 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,7 +1,7 @@
 before_script:
   - module load python/3.6.1-2-anaconda
   - module load nextflow/0.27.6
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_mkfastq/*tar.gz test_data/
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_count/*fastq.gz test_data/
 
 stages:
   - integration
diff --git a/test_data/design.csv b/test_data/design.csv
new file mode 100755
index 0000000..5247791
--- /dev/null
+++ b/test_data/design.csv
@@ -0,0 +1,4 @@
+Sample,fastq_R1,fastq_R2
+D17PrPzF_BE,D17PrPzF_BE_S1_L001_R1_001.fastq.gz,D17PrPzF_BE_S1_L001_R2_001.fastq.gz
+D17PrPzF_BE,D17PrPzF_BE_S1_L002_R1_001.fastq.gz,D17PrPzF_BE_S1_L002_R2_001.fastq.gz
+D17PrPzF_LE,D17PrPzF_LE_S3_L001_R1_001.fastq.gz,D17PrPzF_LE_S3_L001_R2_001.fastq.gz
\ No newline at end of file
-- 
GitLab