Run tabix and report errors (#30)

* Run tabix and report errors * Update to imputationserver-utils v1.5.0 * Disable VCF index creation in validate cmd
genepi · Sep 30, 2024 · 93d5b98 · 93d5b98
1 parent b9f7262
commit 93d5b98
Show file tree

Hide file tree

Showing 4 changed files with 36 additions and 1 deletion.
diff --git a/Dockerfile b/Dockerfile
@@ -48,7 +48,7 @@ RUN wget https://github.com/lukfor/pgs-calc/releases/download/v${PGS_CALC_VERSIO
 ENV PATH="/opt/pgs-calc:${PATH}"
 
 # Install imputationserver-utils
-ENV IMPUTATIONSERVER_UTILS_VERSION=v1.4.5
+ENV IMPUTATIONSERVER_UTILS_VERSION=v1.5.0
 RUN mkdir /opt/imputationserver-utils
 WORKDIR "/opt/imputationserver-utils"
 #COPY files/imputationserver-utils.tar.gz .

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} \
@@ -34,6 +46,7 @@ process INPUT_VALIDATION_VCF {
         --minSamples ${params.min_samples} \
         --maxSamples ${params.max_samples} \
         --report validation_report.txt \
+        --no-index \
         --contactName "${(params.service.contact == "" || params.service.contact == null) ? "Admin" : params.service.contact}" \
         --contactEmail "${(params.service.email == "" || params.service.email == null) ? "admin@localhost" : params.service.email}" \
         $vcf_files 

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
+
+        }
+
+    }   
+
 }