From efbc8c595271b335ef857a4b211faa2daac20981 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 10 Mar 2019 15:29:13 -0500
Subject: [PATCH] Add/update CI with simple tests for kit v 2 and 3, ref v
 1.2.0 and 3.0.0, cellranger v 2 and 3

---
 .gitlab-ci.yml | 27 ++++++++++++++++++++++-----
 1 file changed, 22 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index bd5a7d9..4b00dea 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,13 +1,30 @@
 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_count/*fastq.gz test_data/
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_count/design.csv test_data/
+  - module load nextflow/0.31.1_Ignite
+  - mkdir test_data/v2s2r100k
+  - mkdir test_data/v3s2r100k
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/* test_data/v2s2r100k/
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/* test_data/v3s2r100k/
 
 stages:
   - integration
 
-simple_test:
+simple_cr2v2ref1.2.0:
   stage: integration
   script:
-  - nextflow run workflow/main.nf
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+
+simple_cr2v2ref3.0.0:
+  stage: integration
+  script:
+  - nextflow run workflow/main.nf --fastq = "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome = 'GRCh38-3.0.0' --kitVersion = 'two' --version = '2.1.1'
+
+simple_cr3v2ref3.0.0:
+  stage: integration
+  script:
+  - nextflow run workflow/main.nf --fastq = "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome = 'GRCh38-3.0.0' --kitVersion = 'two' --version = '3.0.2'
+
+simple_cr3v3ref3.0.0:
+  stage: integration
+  script:
+  - nextflow run workflow/main.nf --fastq = "$CI_PROJECT_DIR/test_data/v3s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v3s2r100k/design.csv" --genome = 'GRCh38-3.0.0' --kitVersion = 'three' --version = '3.0.2'
-- 
GitLab