Update GitHub Actions workflow

.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

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 {

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 {