From ea4c12aa2959cee353621b05813a5c99fa99dbe8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Sebastian=20Sch=C3=B6nherr?= <seb.schoenherr@gmail.com>
Date: Tue, 18 Jun 2024 13:50:07 +0200
Subject: [PATCH] Remove unused param

---
 modules/local/lift_over.nf |  4 ++--
 tests/microarray.nf.test   | 19 +++++++++++++++++++
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/modules/local/lift_over.nf b/modules/local/lift_over.nf
index 06c2270..b8d802d 100644
--- a/modules/local/lift_over.nf
+++ b/modules/local/lift_over.nf
@@ -3,10 +3,10 @@ process LIFT_OVER {
 //publishDir "${params.outdir}/aggRSquare", mode: 'copy', pattern: '*aggRSquare'
 
     input:
-    tuple val(chr), val(array_name), path(dosage_data), path(sequence_data)
+    tuple val(chr), path(dosage_data), path(sequence_data)
 
     output:
-    tuple val(chr), val(array_name), path(dosage_data), path("${sequence_data.baseName}.liftover.vcf.gz"), emit: sequence_data_lifted
+    tuple val(chr), path(dosage_data), path("${sequence_data.baseName}.liftover.vcf.gz"), emit: sequence_data_lifted
 
     script:
     def chain_file = (params.sequence_build == 'hg19' ? "/opt/imputationserver/chains/hg19ToHg38.over.chain.gz" : '/opt/imputationserver/chains/hg38ToHg19.over.chain.gz')
diff --git a/tests/microarray.nf.test b/tests/microarray.nf.test
index f380d52..31ad811 100644
--- a/tests/microarray.nf.test
+++ b/tests/microarray.nf.test
@@ -71,4 +71,23 @@ nextflow_pipeline {
 
     }
 
+    test("Rsq calculation for hg19/hg38") {
+
+        when {
+            params {
+               project          = "r2_calculation_hg19"
+               workflow_name    = "r2"
+               imputation_build = "hg19"
+               sequence_build   = "hg38"
+               imputed_data     = "$projectDir/tests/data/imputed_data/hg19/*vcf.gz"
+               sequence_data    = "$projectDir/tests/data/sequence_data/hg38/*vcf.gz"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
 }
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