From 2b7945ae24e43473a36b5ebc5149fc0601a31ee1 Mon Sep 17 00:00:00 2001
From: Emilio Palumbo <emiliopalumbo@gmail.com>
Date: Mon, 17 Jun 2024 20:30:47 +0200
Subject: [PATCH] Update GitHub Actions workflow

---
 .github/workflows/test.yml | 5 ++---
 nextflow.config            | 8 ++++----
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 7d5dfff..e34c591 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -17,8 +17,8 @@ jobs:
   pipeline-test:
     name: Pipeline tests
     runs-on: ubuntu-latest
-    needs: workflow-test
-
+    needs: [module-test, workflow-test]
+    
     strategy:
       fail-fast: false
       matrix:
@@ -50,7 +50,6 @@ jobs:
   workflow-test:
     name: Workflow tests
     runs-on: ubuntu-latest
-    needs: module-test
 
     steps:
       - uses: actions/checkout@v4
diff --git a/nextflow.config b/nextflow.config
index 86ed900..da60293 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -6,12 +6,12 @@ manifest.mainScript = 'grape-pipeline.nf'
 
 // small input dataset for testing
 params {
-        index = "$baseDir/test-index.txt"
-        genome = "$baseDir/data/genome.fa"
-        annotation = "$baseDir/data/annotation.gtf"
+    index = "$baseDir/test-index.txt"
+    genome = "$baseDir/data/genome.fa"
+    annotation = "$baseDir/data/annotation.gtf"
 }
 
-params.containerRepo = "public.ecr.aws/biocontainers"
+params.containerRepo = "quay.io/biocontainers"
 
 // Docker is disabled by default and uses the following options when activated
 docker {