From cbe455cb3b0e21cf53181100f31141db5c37df79 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 12 Feb 2024 18:32:45 +0100
Subject: [PATCH] update data path

---
 .../samtools/flagstat/tests/main.nf.test      | 12 +++++------
 .../samtools/flagstat/tests/main.nf.test.snap | 20 +++++++++++++++++--
 2 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test
index c8dd8dc9feb..24c3c04b09b 100644
--- a/modules/nf-core/samtools/flagstat/tests/main.nf.test
+++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test
@@ -16,11 +16,11 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ 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)
-                ]
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ])
                 """
             }
         }
@@ -28,8 +28,8 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out.flagstat).match() },
-                { assert path(process.out.versions.get(0)).getText().contains("samtools") }
+                { assert snapshot(process.out.flagstat).match("flagstat") },
+                { assert snapshot(process.out.versions).match("versions") }
             )
         }
     }
diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
index 880019f2f2b..43f3bc2c3fc 100644
--- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "BAM": {
+    "flagstat": {
         "content": [
             [
                 [
@@ -11,6 +11,22 @@
                 ]
             ]
         ],
-        "timestamp": "2023-11-14T15:49:22.577133"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T18:31:37.783927"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,27815e477dcca61cd6b5ca2a94993965"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-02-12T18:31:37.788139"
     }
 }
\ No newline at end of file