Run tabix and report errors

genepi · Sep 30, 2024 · cfe2218 · cfe2218
1 parent 98e3059
commit cfe2218
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diff --git a/modules/local/input_validation/input_validation_vcf.nf b/modules/local/input_validation/input_validation_vcf.nf
@@ -24,6 +24,18 @@ process INPUT_VALIDATION_VCF {
     set +e
     echo '${JsonOutput.toJson(params.refpanel)}' > reference-panel.json
 
+    # Verify if VCF files are valid
+    for vcf in "$vcf_files"; do
+        # Attempt to create the index using tabix
+        if ! output=\$(tabix -p vcf "\$vcf" 2>&1); then
+            echo ::group type=error
+            echo "The provided VCF file is malformed."
+            echo "Error: \$output"
+            echo ::endgroup::
+            exit 1
+        fi
+    done
+
     java -Xmx${avail_mem}M -jar /opt/imputationserver-utils/imputationserver-utils.jar \
         validate \
         --population ${params.population} \

diff --git a/tests/data/input/invalid-vcfs/unsorted.vcf.gz b/tests/data/input/invalid-vcfs/unsorted.vcf.gz
diff --git a/tests/main.validate.nf.test b/tests/main.validate.nf.test
@@ -23,4 +23,26 @@ nextflow_pipeline {
 
     }
 
+
+    test("Should fail due to unsorted file") {
+
+        when {
+            params {
+                project  = "test-job"
+                build = "hg19"
+                files = "$projectDir/tests/data/input/invalid-vcfs/unsorted.vcf.gz"
+                allele_frequency_population = "eur"
+                mode = "qc-only"
+                refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap2/cloudgene.yaml"
+                output = "${outputDir}"
+            }   
+        }
+
+        then {
+            assert workflow.failed
+
+        }
+
+    }   
+
 }