From 09d4e0166f9081e46af20e0e4bd70ea68532d97e 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 ++---
 modules/inferExp/rseqc/main.nf | 2 +-
 nextflow.config                | 8 ++++----
 3 files changed, 7 insertions(+), 8 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/modules/inferExp/rseqc/main.nf b/modules/inferExp/rseqc/main.nf
index cb4fc61..08b25c9 100644
--- a/modules/inferExp/rseqc/main.nf
+++ b/modules/inferExp/rseqc/main.nf
@@ -2,7 +2,7 @@ params.rseqcVersion = '2.6.4--py27hf8a1672_2'
 params.ucscVersion = '447--h2a80c09_1'
 params.gtfToGenePredContainer = "${params.containerRepo}/ucsc-gtftogenepred:${params.ucscVersion}"
 params.genePredContainer = "${params.containerRepo}/ucsc-genepredtobed:${params.ucscVersion}"
-params.rseqcContainer = "${params.containerRepo}/rseqc:${params.rseqcVersion}"
+params.rseqcContainer = "public.ecr.aws/biocontainers/rseqc:${params.rseqcVersion}"
 params.inferExpThreshold = '0.8'
 
 process gtfToGenePred {
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 {