tests/data/input/chrX-phased/vcf_v4.3/small.chrX.vcf.gz

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tests/main.imputation.nf.test

-Original file line number
+Diff line change
@@ Expand Up / @@ -801,6 +801,42 @@ nextflow_pipeline { @@
         }
+        test("Should run with phased chrX data with VCF v4.3 and hg38") {
+            when {
+                params {
+                    project  = "testChrXPipelineWithPhasedHg38"
+                    build = "hg19"
+                    files = "$projectDir/tests/data/input/chrX-phased/vcf_v4.3/*.vcf.gz"
+                    allele_frequency_population = "eur"
+                    password = PASSWORD
+                    refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap-chrX-hg38/cloudgene.yaml"
+                    output = "${outputDir}"
+                    phasing = [
+                        engine: "no_phasing"
+                    ]
+                }
+            }
+            then {
+                assert workflow.success
+                def zip = zip("${outputDir}/chr_X.zip").password(PASSWORD)
+                with(zip) {
+                    assert isValid()
+                    assert isEncrypted()
+                }
+                with(zip.extract("chrX.dose.vcf.gz").vcf) {
+                    assert chromosome == "chrX"
+                    assert sampleCount == 26;
+                    assert phased
+                    assert variantCount == TOTAL_REFPANEL_CHRX_B38
+                }
+            }
+        }
         test("Should run with phased chr23 data and hg38") {
@@ Expand Down @@

Add testcase using VCF 4.3 data #32

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seppinho wants to merge 2 commits into main from fixes/liftover-index-creation

-Original file line number
+Diff line change
@@ Expand Up / @@ -801,6 +801,42 @@ nextflow_pipeline { @@
         }
+        test("Should run with phased chrX data with VCF v4.3 and hg38") {
+            when {
+                params {
+                    project  = "testChrXPipelineWithPhasedHg38"
+                    build = "hg19"
+                    files = "$projectDir/tests/data/input/chrX-phased/vcf_v4.3/*.vcf.gz"
+                    allele_frequency_population = "eur"
+                    password = PASSWORD
+                    refpanel_yaml = "$projectDir/tests/data/refpanels/hapmap-chrX-hg38/cloudgene.yaml"
+                    output = "${outputDir}"
+                    phasing = [
+                        engine: "no_phasing"
+                    ]
+                }
+            }
+            then {
+                assert workflow.success
+                def zip = zip("${outputDir}/chr_X.zip").password(PASSWORD)
+                with(zip) {
+                    assert isValid()
+                    assert isEncrypted()
+                }
+                with(zip.extract("chrX.dose.vcf.gz").vcf) {
+                    assert chromosome == "chrX"
+                    assert sampleCount == 26;
+                    assert phased
+                    assert variantCount == TOTAL_REFPANEL_CHRX_B38
+                }
+            }
+        }
         test("Should run with phased chr23 data and hg38") {
@@ Expand Down @@

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