From c469a2b35ed2e2948c9d3cbde5672143086b7e35 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 2 Jun 2022 20:32:00 +0200
Subject: [PATCH] Fux tests

---
 modules/gatk/realignertargetcreator/main.nf   |  6 +++---
 .../gatk/realignertargetcreator/main.nf       | 19 ++++++++-----------
 2 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/modules/gatk/realignertargetcreator/main.nf b/modules/gatk/realignertargetcreator/main.nf
index 866ff8a5..e356c826 100644
--- a/modules/gatk/realignertargetcreator/main.nf
+++ b/modules/gatk/realignertargetcreator/main.nf
@@ -9,7 +9,7 @@ process GATK_REALIGNERTARGETCREATOR {
 
     input:
     tuple val(meta), path(input), path(index)
-    path path(fasta)
+    path(fasta)
     path(fai)
     path(dict)
     path(known_vcf)
@@ -25,7 +25,7 @@ process GATK_REALIGNERTARGETCREATOR {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def known = known_vcf ? "-known ${known_vcf}" : ""
-    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
     def avail_mem = 3
     if (!task.memory) {
@@ -39,7 +39,7 @@ process GATK_REALIGNERTARGETCREATOR {
         -Xmx${avail_mem}g \\
         -T RealignerTargetCreator \\
         -nt ${task.cpus} \\
-        -I ${bam} \\
+        -I ${input} \\
         -R ${fasta} \\
         -o ${prefix}.intervals \\
         ${known} \\
diff --git a/tests/modules/gatk/realignertargetcreator/main.nf b/tests/modules/gatk/realignertargetcreator/main.nf
index 02e62d93..4b9f8eff 100644
--- a/tests/modules/gatk/realignertargetcreator/main.nf
+++ b/tests/modules/gatk/realignertargetcreator/main.nf
@@ -6,16 +6,13 @@ include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realigner
 
 workflow test_gatk_realignertargetcreator {
 
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
-    ]
-    reference = [
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true),
-    ]
+    input     = [ [ id:'test' ], // meta map
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
 
-    GATK_REALIGNERTARGETCREATOR ( input, reference, [] )
+    GATK_REALIGNERTARGETCREATOR ( input, fasta, fai, dict, [] )
 }