From bb378a158adcc07aeb20db954c53226ef14e9fb1 Mon Sep 17 00:00:00 2001
From: Samuel Lampa <samuel.lampa@scilifelab.se>
Date: Mon, 4 Nov 2024 13:34:21 +0100
Subject: [PATCH] Fix command

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d6dcd1e..dc483a0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -60,8 +60,9 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run main.nf \
+          nextflow  \
             -log $(pwd)/nextflow.log \
+            run main.nf \
             --outdir results \
             --db $(pwd)/assets/databases/emu_database \
             --seqtype map-ont \