From 641c44e502af7ed1fda4fd71189de562b88766de Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Mon, 26 Aug 2024 14:17:10 +1200
Subject: [PATCH] Added nf-test for bcftools/split

---
 .../nf-core/bcftools/split/tests/main.nf.test | 40 +++++++++++++++++++
 .../bcftools/split/tests/main.nf.test.snap    | 15 +++++++
 tests/config/pytest_modules.yml               |  3 --
 tests/modules/nf-core/bcftools/split/main.nf  | 16 --------
 .../nf-core/bcftools/split/nextflow.config    |  5 ---
 tests/modules/nf-core/bcftools/split/test.yml |  8 ----
 6 files changed, 55 insertions(+), 32 deletions(-)
 create mode 100644 modules/nf-core/bcftools/split/tests/main.nf.test
 create mode 100644 modules/nf-core/bcftools/split/tests/main.nf.test.snap
 delete mode 100644 tests/modules/nf-core/bcftools/split/main.nf
 delete mode 100644 tests/modules/nf-core/bcftools/split/nextflow.config
 delete mode 100644 tests/modules/nf-core/bcftools/split/test.yml

diff --git a/modules/nf-core/bcftools/split/tests/main.nf.test b/modules/nf-core/bcftools/split/tests/main.nf.test
new file mode 100644
index 00000000000..00328b2004c
--- /dev/null
+++ b/modules/nf-core/bcftools/split/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+    name "Test Process BCFTOOLS_SPLIT"
+    script "../main.nf"
+    process "BCFTOOLS_SPLIT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/split"
+
+    test("test-bcftools-split") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.split_vcf[0][1]).vcf.variantsMD5,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bcftools/split/tests/main.nf.test.snap b/modules/nf-core/bcftools/split/tests/main.nf.test.snap
new file mode 100644
index 00000000000..c1a3c98578c
--- /dev/null
+++ b/modules/nf-core/bcftools/split/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+    "test-bcftools-split": {
+        "content": [
+            "ecf3973f634b7baa1c13e60bfb77a174",
+            [
+                "versions.yml:md5,a1c58d82f1e5c0fed394bfb865f57fd9"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T14:16:45.077115"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4aea9c2af1e..e7870279f1c 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -88,9 +88,6 @@ bcftools/merge:
 bcftools/roh:
   - modules/nf-core/bcftools/roh/**
   - tests/modules/nf-core/bcftools/roh/**
-bcftools/split:
-  - modules/nf-core/bcftools/split/**
-  - tests/modules/nf-core/bcftools/split/**
 beagle5/beagle:
   - modules/nf-core/beagle5/beagle/**
   - tests/modules/nf-core/beagle5/beagle/**
diff --git a/tests/modules/nf-core/bcftools/split/main.nf b/tests/modules/nf-core/bcftools/split/main.nf
deleted file mode 100644
index 6304841ca82..00000000000
--- a/tests/modules/nf-core/bcftools/split/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_SPLIT } from '../../../../../modules/nf-core/bcftools/split/main.nf'
-
-workflow test_bcftools_split {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    BCFTOOLS_SPLIT ( input )
-}
diff --git a/tests/modules/nf-core/bcftools/split/nextflow.config b/tests/modules/nf-core/bcftools/split/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/bcftools/split/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bcftools/split/test.yml b/tests/modules/nf-core/bcftools/split/test.yml
deleted file mode 100644
index d4178a52b41..00000000000
--- a/tests/modules/nf-core/bcftools/split/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: bcftools split test_bcftools_split
-  command: nextflow run ./tests/modules/nf-core/bcftools/split -entry test_bcftools_split -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/split/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/split
-  files:
-    - path: output/bcftools/test.chr22.vcf.gz
-    - path: output/bcftools/versions.yml