Commit 8e7ac5e9 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Add split unit tests for modules and containers

parent bc18bf72
Pipeline #7795 failed with stages
in 14 minutes and 13 seconds
......@@ -3,7 +3,7 @@ before_script:
- module load python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- module load nextflow/20.01.0
- module load singularity/3.0.2
- module load singularity/3.5.3
- mkdir -p test_data/hu.v2s1r500
- mkdir -p test_data/hu.v3s1r500
- mkdir -p test_data/mu.v3s1r500
......@@ -19,6 +19,7 @@ before_script:
stages:
- astrocyte_test
- module_test
- container_test
- reference_test
- multiSample_test
......@@ -34,8 +35,8 @@ astrocyte_cli:
when:
- always
2.1.1_test:
stage: container_test
module_2.1.1_test:
stage: module_test
only:
- branches
except:
......@@ -57,8 +58,8 @@ astrocyte_cli:
when:
- always
3.0.2_test:
stage: container_test
module_3.0.2_test:
stage: module_test
only:
- branches
except:
......@@ -80,8 +81,8 @@ astrocyte_cli:
when:
- always
3.1.0_test:
stage: container_test
module_3.1.0_test:
stage: module_test
only:
- branches
except:
......@@ -105,8 +106,8 @@ astrocyte_cli:
when:
- always
4.0.0_test:
stage: container_test
module_4.0.0_test:
stage: module_test
only:
- branches
except:
......@@ -130,6 +131,98 @@ astrocyte_cli:
when:
- always
container_2.1.1_test:
stage: container_test
only:
- branches
except:
refs:
- develop
- master
- tags
script:
- singularity run 'docker://bicf/cellranger2.1.1:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- test/outs/web_summary.html
expire_in: 2 days
retry:
max: 0
when:
- always
container_3.0.2_test:
stage: container_test
only:
- branches
except:
refs:
- develop
- master
- tags
script:
- singularity run 'docker://bicf/cellranger3.0.2:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- test/outs/web_summary.html
expire_in: 2 days
retry:
max: 0
when:
- always
container_3.1.0_test:
stage: container_test
only:
- branches
except:
refs:
- develop
- master
- tags
script:
- singularity run 'docker://bicf/cellranger3.1.0:2.0.0' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0 --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- develop
- master
- test/outs/web_summary.html
expire_in: 2 days
retry:
max: 0
when:
- always
container_4.0.0_test:
stage: container_test
only:
- branches
except:
refs:
- develop
- master
- tags
script:
- singularity run 'docker://bicf/cellranger4.0.0:2.0.0_indev' cellranger count --id=test --transcriptome=/project/apps_database/cellranger/refdata-gex-GRCh38-2020-A --fastqs=./test_data/hu.v2s1r500 --sample=pbmc_1k_v2 --chemistry=SC3Pv2
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- develop
- master
- test/outs/web_summary.html
expire_in: 2 days
retry:
max: 0
when:
- always
GRCh38-2020A:
stage: reference_test
only:
......
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