Switch to variable based command

2021-03-17 11:06:24 +00:00 · 2021-03-17 11:06:24 +00:00 · fba94dcd8f
commit fba94dcd8f
parent f7aa07209b
1 changed files with 2 additions and 13 deletions
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@ -2,17 +2,6 @@ include:
    - project: "epi2melabs/ci-templates"
      file: "wf-containers.yaml"

-.run: &run |
-    ${NEXTFLOWRUN} -w ${OUTPUT}/workspace --out_dir ${OUTPUT} \
-        --fastq test_data
+variables:
+    NF_WORKFLOW_OPTS: "--fastq test_data"

-conda-run:
-    extends: .conda-run
-    script:
-        - *run
-
-docker-run:
-    extends: .docker-run
-    script:
-        - *run
-        - touch ${CI_PROJECT_DIR}/success