Commit 7599692c authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Git module and container unit tests for seurat

parent d262bb16
Pipeline #7871 failed with stages
in 4 seconds
......@@ -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:
......
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