From fba94dcd8f49243a2706164c222988c5c1ecd568 Mon Sep 17 00:00:00 2001
From: Chris Wright <chris.wright@nanoporetech.com>
Date: Wed, 17 Mar 2021 11:06:24 +0000
Subject: [PATCH] Switch to variable based command

---
 .gitlab-ci.yml | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c37dfb6..817d906 100644
--- 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