diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 06213a0795994e0662c8a3e3ff75a4cfac134cdf..fb0324af15bc1f21905c8d3a2ec8ab8d8f091e8e 100755 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -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: