diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index bfc71b3c897e65d93dcca03ad944873142478a5c..e1b45b57442997107b542a371a47dec26898d039 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -2,16 +2,12 @@ # Brandi L. Cantarel - 2017 variables: - RUNDIR: "/project/BICF/BICF_Core/shared/astrocyte_test_ci/rnaseq_test" TEST_BRANCH: "master" GIT_SUBMODULE_STATEGY: recursive before_script: - module load nextflow/0.27.6 - - mkdir -p "${RUNDIR}" - - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/* ${RUNDIR}/test_data/ - - echo $RUNDIR - - ls -l ${RUNDIR}/test_data/ + - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq test_data stages: - integration @@ -19,17 +15,13 @@ stages: test_human: stage: integration script: - - nextflow run workflow/main.nf --design ${RUNDIR}/test_data/design.rnaseq.txt --input ${RUNDIR}/test_data --output ${RUNDIR}/human_output + - nextflow run workflow/main.nf --design test_data/design.rnaseq.txt --input test_data --output human_output artifacts: - paths: - - ${RUNDIR} expire_in: 2 days test_mouse: stage: integration script: - - nextflow run workflow/main.nf --input ${RUNDIR}/test_data --design ${RUNDIR}/test_data/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output ${RUNDIR}/mouse_output + - 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 artifacts: - paths: - - ${RUNDIR} expire_in: 2 days