From 6068a2bced963354a8409bdd84a4fbdcc672b50a Mon Sep 17 00:00:00 2001
From: Ksenia Krasheninnikova <kk16@sanger.ac.uk>
Date: Wed, 26 Jul 2023 13:34:15 +0100
Subject: [PATCH] Fix data references

---
 tests/config/test_data.config                    | 8 ++++++++
 tests/modules/nf-core/mitohifi/mitohifi/main.nf  | 6 +++---
 tests/modules/nf-core/mitohifi/mitohifi/test.yml | 2 +-
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 7dd758a8156..38800069c2e 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -637,6 +637,14 @@ params {
                 pretext = "${params.test_data_base}/data/genomics/eukaryotes/galaxea_fascicularis/hic/jaGalFasc40_2.pretext"
             }
         }
+        'deilephila_porcellus' {
+            'mito' {
+                ref_fa      = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.fasta"
+                ref_gb      = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/MW539688.1.gb"
+                hifi_reads  = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.HiFi.reads.fa"
+                contigs     = "${params.test_data_base}/data/genomics/eukaryotes/deilephila_porcellus/mito/ilDeiPorc1.contigs.fa"
+            }
+        }
         'imaging' {
             'h5' {
                 plant_wga                       = "${params.test_data_base}/data/imaging/h5/plant_wga.h5"
diff --git a/tests/modules/nf-core/mitohifi/mitohifi/main.nf b/tests/modules/nf-core/mitohifi/mitohifi/main.nf
index 0837ce4b715..48c127b7d17 100644
--- a/tests/modules/nf-core/mitohifi/mitohifi/main.nf
+++ b/tests/modules/nf-core/mitohifi/mitohifi/main.nf
@@ -8,9 +8,9 @@ workflow test_mitohifi_mitohifi {
     
     species = "'Deilephila porcellus'"
 
-    data_contigs = Channel.of([[id:"ilDeiPorc1"],[],file(params.test_data['eukaryotes']['deilephila_porcellus']['mito']['ilDeiPorc1.contigs.fa'], checkIfExists: true)])
-    ref_gb = file(params.test_data['eukaryotes']['deilephila_porcells']['mito']['MW539688.1.gb'], checkIfExists: true)
-    ref_gb = file(params.test_data['eukaryotes']['deilephila_porcells']['mito']['MW539688.1.fasta'], checkIfExists: true)
+    data_contigs = Channel.of([[id:"ilDeiPorc1"],[],file(params.test_data['deilephila_porcellus']['mito']['contigs'], checkIfExists: true)])
+    ref_gb = file(params.test_data['deilephila_porcellus']['mito']['ref_gb'], checkIfExists: true)
+    ref_fa = file(params.test_data['deilephila_porcellus']['mito']['ref_fa'], checkIfExists: true)
     code = 5
     MITOHIFI_MITOHIFI ( data_contigs, ref_fa, ref_gb, code )
 }
diff --git a/tests/modules/nf-core/mitohifi/mitohifi/test.yml b/tests/modules/nf-core/mitohifi/mitohifi/test.yml
index 8db6bc12074..cac258cc533 100644
--- a/tests/modules/nf-core/mitohifi/mitohifi/test.yml
+++ b/tests/modules/nf-core/mitohifi/mitohifi/test.yml
@@ -5,7 +5,7 @@
     - mitohifi/mitohifi
   files:
     - path: output/mitohifi/contigs_stats.tsv
-      md5sum: 1db72e07023dadaea9d9c5086c243203
+      md5sum: 4b1a80bf2049e9facb04e7d2e99409d2
     - path: output/mitohifi/final_mitogenome.fasta
       md5sum: 5654c418bbf991483d9e618dd849af03
     - path: output/mitohifi/final_mitogenome.gb