From 7599692c267489cda35fe10a8dfa73ccec70b528 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 14 Aug 2020 13:03:51 -0500
Subject: [PATCH] Git module and container unit tests for seurat
---
.gitlab-ci.yml | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 50 insertions(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0d39b4e..2ea2354 100755
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -16,6 +16,7 @@ before_script:
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v3s2r10k/* test_data/hu.v3s2r10k/
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/mu.v3s2r10k/* test_data/mu.v3s2r10k/
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/hu.v2s2r10k/* test_data/hu.v2s2r10k/
+ - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/output/* test_data/output/
stages:
- astrocyte_test
@@ -127,6 +128,31 @@ module_4.0.0_test:
when:
- always
+module_seurat_test:
+ stage: module_test
+ only:
+ - branches
+ except:
+ refs:
+ - develop
+ - master
+ - tags
+ script:
+ - module load seurat/3.0.0
+ - ln -s test-data/output/* .
+ - seurat-Rscript workflow/scripts/downstream_viz.r --sample sample1 --cellrangerVersion 4.0.0
+ - bash workflow/scripts/versions_seurat.sh > version_seurat.txt
+ artifacts:
+ name: "$CI_JOB_NAME"
+ when: always
+ paths:
+ - version_seurat.txt
+ expire_in: 2 days
+ retry:
+ max: 0
+ when:
+ - always
+
container_2.1.1_test:
stage: container_test
only:
@@ -215,6 +241,30 @@ container_4.0.0_test:
when:
- always
+container_seurat_test:
+ stage: module_test
+ only:
+ - branches
+ except:
+ refs:
+ - develop
+ - master
+ - tags
+ script:
+ - ln -s test-data/output/* .
+ - singularity run 'docker://bicf/seurat:2.0.0_indev' Rscript workflow/scripts/downstream_viz.r --sample sample1 --cellrangerVersion 4.0.0
+ - singularity run 'docker://bicf/seurat:2.0.0_indev' bash workflow/scripts/versions_seurat.sh > version_seurat.txt
+ artifacts:
+ name: "$CI_JOB_NAME"
+ when: always
+ paths:
+ - version_seurat.txt
+ expire_in: 2 days
+ retry:
+ max: 0
+ when:
+ - always
+
GRCh38-2020A:
stage: reference_test
only:
--
GitLab