update gitlab-ci.yml

.gitlab-ci.yml

@@ -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