diff --git a/tests/data/input/chrX-phased/vcf_v4.3/small.chrX.vcf.gz b/tests/data/input/chrX-phased/vcf_v4.3/small.chrX.vcf.gz new file mode 100644 index 0000000..14748f4 Binary files /dev/null and b/tests/data/input/chrX-phased/vcf_v4.3/small.chrX.vcf.gz differ diff --git a/tests/main.imputation.nf.test b/tests/main.imputation.nf.test index c1bdfcd..2425b64 100644 --- a/tests/main.imputation.nf.test +++ b/tests/main.imputation.nf.test @@ -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") {