diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index c25db0377fe06e4c53a44defe8e791d372d3bf20..49bd46f113baf053350e564089178df6185a6a3a 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -7,6 +7,7 @@ variables: before_script: - module load nextflow/0.27.6 + - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq test_data stages: - integration @@ -14,13 +15,13 @@ stages: test_human: stage: integration script: - - nextflow run workflow/main.nf --design test_data/design.rnaseq.txt --input test_data --output human_output + - nextflow run workflow/main.nf --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/design.rnaseq.txt --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --output human_output artifacts: expire_in: 2 days test_mouse: stage: integration script: - - nextflow run workflow/main.nf --input test_data --design test_data/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output mouse_output + - nextflow run workflow/main.nf --input /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --design /project/shared/bicf_workflow_ref/workflow_testdata/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output mouse_output artifacts: expire_in: 2 days