From 176c11c82a322a6882d3c3529d3791e823b6976d Mon Sep 17 00:00:00 2001
From: Felix Lenner <52530259+fellen31@users.noreply.github.com>
Date: Tue, 19 Mar 2024 13:00:18 +0100
Subject: [PATCH] Add nf-test to minimap2 index (#5189)

* Add nf-test to minimap2 index

* correct tags

* remove pytest

* remove quotation marks
---
 .../nf-core/minimap2/index/tests/main.nf.test | 32 +++++++++
 .../minimap2/index/tests/main.nf.test.snap    | 68 +++++++++++++++++++
 modules/nf-core/minimap2/index/tests/tags.yml |  2 +
 tests/config/pytest_modules.yml               |  3 -
 tests/modules/nf-core/minimap2/index/main.nf  | 12 ----
 .../nf-core/minimap2/index/nextflow.config    |  5 --
 tests/modules/nf-core/minimap2/index/test.yml |  8 ---
 7 files changed, 102 insertions(+), 28 deletions(-)
 create mode 100644 modules/nf-core/minimap2/index/tests/main.nf.test
 create mode 100644 modules/nf-core/minimap2/index/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/minimap2/index/tests/tags.yml
 delete mode 100644 tests/modules/nf-core/minimap2/index/main.nf
 delete mode 100644 tests/modules/nf-core/minimap2/index/nextflow.config
 delete mode 100644 tests/modules/nf-core/minimap2/index/test.yml

diff --git a/modules/nf-core/minimap2/index/tests/main.nf.test b/modules/nf-core/minimap2/index/tests/main.nf.test
new file mode 100644
index 00000000000..97840ff75d0
--- /dev/null
+++ b/modules/nf-core/minimap2/index/tests/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process MINIMAP2_INDEX"
+    script "../main.nf"
+    process "MINIMAP2_INDEX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "minimap2"
+    tag "minimap2/index"
+
+    test("minimap2 index") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/minimap2/index/tests/main.nf.test.snap b/modules/nf-core/minimap2/index/tests/main.nf.test.snap
new file mode 100644
index 00000000000..454c834f216
--- /dev/null
+++ b/modules/nf-core/minimap2/index/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_ref"
+                        },
+                        "genome.mmi:md5,72e450f12dc691e763c697463bdb1571"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0fced0ee8015e7f50b82566e3db8f7b0"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test_ref"
+                        },
+                        "genome.mmi:md5,72e450f12dc691e763c697463bdb1571"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0fced0ee8015e7f50b82566e3db8f7b0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T11:46:30.000058092"
+    },
+    "minimap2 index": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.mmi:md5,72e450f12dc691e763c697463bdb1571"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0fced0ee8015e7f50b82566e3db8f7b0"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.mmi:md5,72e450f12dc691e763c697463bdb1571"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0fced0ee8015e7f50b82566e3db8f7b0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T13:41:53.865122291"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/minimap2/index/tests/tags.yml b/modules/nf-core/minimap2/index/tests/tags.yml
new file mode 100644
index 00000000000..e5ef8e19f3f
--- /dev/null
+++ b/modules/nf-core/minimap2/index/tests/tags.yml
@@ -0,0 +1,2 @@
+minimap2/index:
+  - modules/nf-core/minimap2/index/**
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 85ec8d8253d..fa95fc6f07e 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1361,9 +1361,6 @@ minia:
 miniasm:
   - modules/nf-core/miniasm/**
   - tests/modules/nf-core/miniasm/**
-minimap2/index:
-  - modules/nf-core/minimap2/index/**
-  - tests/modules/nf-core/minimap2/index/**
 miniprot/align:
   - modules/miniprot/align/**
   - tests/modules/miniprot/align/**
diff --git a/tests/modules/nf-core/minimap2/index/main.nf b/tests/modules/nf-core/minimap2/index/main.nf
deleted file mode 100644
index 212bb64e0ee..00000000000
--- a/tests/modules/nf-core/minimap2/index/main.nf
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { MINIMAP2_INDEX } from '../../../../../modules/nf-core/minimap2/index/main.nf'
-
-workflow test_minimap2_index {
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-
-    MINIMAP2_INDEX ( [ [id:'test'], fasta ] )
-}
diff --git a/tests/modules/nf-core/minimap2/index/nextflow.config b/tests/modules/nf-core/minimap2/index/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/minimap2/index/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/minimap2/index/test.yml b/tests/modules/nf-core/minimap2/index/test.yml
deleted file mode 100644
index a2e0199b8f0..00000000000
--- a/tests/modules/nf-core/minimap2/index/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: minimap2 index
-  command: nextflow run ./tests/modules/nf-core/minimap2/index -entry test_minimap2_index -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/minimap2/index/nextflow.config
-  tags:
-    - minimap2
-    - minimap2/index
-  files:
-    - path: ./output/minimap2/genome.mmi
-      md5sum: 72e450f12dc691e763c697463bdb1571