Remove unused param

genepi · Jun 18, 2024 · ea4c12a · ea4c12a
1 parent af2496c
commit ea4c12a
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Showing 2 changed files with 21 additions and 2 deletions.
diff --git 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
@@ -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
+        }
+
+    }
+
 }