Fix loop iteration

genepi · Sep 30, 2024 · f1862f2 · f1862f2
1 parent 04bf59d
commit f1862f2
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Showing 2 changed files with 23 additions and 4 deletions.
diff --git a/modules/local/input_validation/input_validation_vcf.nf b/modules/local/input_validation/input_validation_vcf.nf
@@ -25,7 +25,7 @@ process INPUT_VALIDATION_VCF {
     echo '${JsonOutput.toJson(params.refpanel)}' > reference-panel.json
 
     # Verify if VCF files are valid
-    for vcf in "$vcf_files"; do
+    for vcf in $vcf_files; do
         # Attempt to create the index using tabix
         if ! output=\$(tabix -p vcf "\$vcf" 2>&1); then
             echo ::group type=error

diff --git a/tests/main.validate.nf.test b/tests/main.validate.nf.test
@@ -3,13 +3,33 @@ nextflow_pipeline {
     name "Pipeline Tests for Input Validation"
     script "main.nf"
 
+    test("Should pass with several files") {
+
+        when {
+            params {
+                project  = "test-job"
+                build = "hg19"
+                files = "$projectDir/tests/data/input/three/*.vcf.gz"
+                allele_frequency_population = "eur"
+                mode = "qc-only"
+                refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap2/cloudgene.yaml"
+                output = "${outputDir}"
+            }   
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
     test("Should fail due to wrong path") {
 
         when {
             params {
                 project  = "test-job"
                 build = "hg19"
-                files = "$projectDir/tests/data/input/chr20-phased/*.vcf.gzz"
+                files = "$projectDir/tests/data/input/chr20-phased/*.vcf.gz"
                 allele_frequency_population = "eur"
                 mode = "qc-only"
                 refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap2/cloudgene.yaml"
@@ -23,14 +43,13 @@ nextflow_pipeline {
 
     }
 
-
     test("Should fail due to unsorted file") {
 
         when {
             params {
                 project  = "test-job"
                 build = "hg19"
-                files = "$projectDir/tests/data/input/invalid-vcfs/unsorted.vcf.gz"
+                files = "$projectDir/tests/data/input/invalid-vcfs/*.vcf.gz"
                 allele_frequency_population = "eur"
                 mode = "qc-only"
                 refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap2/cloudgene.yaml"