Commit 8747d42f authored by Brandi Cantarel's avatar Brandi Cantarel
Browse files

update gitlab-ci.yml

parent f0b20683
Pipeline #1656 failed with stage
in 1 minute and 3 seconds
......@@ -2,13 +2,14 @@
# Brandi L. Cantarel - 2017
variables:
CLEAN_REPO_PATH: "/project/BICF/BICF_Core/s166458/astrocyte_test/${CI_RUNNER_ID}"
RUNDIR: "/project/BICF/BICF_Core/shared/astrocyte_test_ci/rnaseq_test"
TEST_BRANCH: "master"
before_script:
- module load nextflow/0.27.6
- mkdir -p "${CLEAN_REPO_PATH}"
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq ${CLEAN_REPO_PATH}/test_data
- mkdir -p "${RUNDIR}"
- echo $RUNDIR
- ln -s /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq ${RUNDIR}/test_data
stages:
- integration
......@@ -16,17 +17,17 @@ stages:
test_human:
stage: integration
script:
- nextflow run workflow/main.nf --input test_data/ --design ${CLEAN_REPO_PATH}/test_data/design.rnaseq.txt --output ${CLEAN_REPO_PATH}/human_output
- nextflow run workflow/main.nf --design ${RUNDIR}/test_data/design.rnaseq.txt --input ${RUNDIR}/test_data --output ${RUNDIR}/human_output
artifacts:
paths:
- ${CLEAN_REPO_PATH}
- ${RUNDIR}
expire_in: 2 days
test_mouse:
stage: integration
script:
- nextflow run workflow/main.nf --input test_data/ --design ${CLEAN_REPO_PATH}/test_data/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/GRCm38 --markdups null --output ${CLEAN_REPO_PATH}/mouse_output
- 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
artifacts:
paths:
- ${CLEAN_REPO_PATH}
- ${RUNDIR}
expire_in: 2 days
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