From 2a6fda4131ae1a389fe5c04e17018ed5418c5549 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Mon, 26 Aug 2024 18:35:10 +1200
Subject: [PATCH] Added nf-test for bam2fastx/bam2fastq (#6343)

* Added nf-test for bam2fastx/bam2fastq

* Swap to snapshot all

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 .../bam2fastx/bam2fastq/tests/main.nf.test    | 37 +++++++++++++++++++
 .../bam2fastq/tests/main.nf.test.snap         | 35 ++++++++++++++++++
 tests/config/pytest_modules.yml               |  3 --
 .../nf-core/bam2fastx/bam2fastq/main.nf       | 16 --------
 .../bam2fastx/bam2fastq/nextflow.config       |  5 ---
 .../nf-core/bam2fastx/bam2fastq/test.yml      |  9 -----
 6 files changed, 72 insertions(+), 33 deletions(-)
 create mode 100644 modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test
 create mode 100644 modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap
 delete mode 100644 tests/modules/nf-core/bam2fastx/bam2fastq/main.nf
 delete mode 100644 tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config
 delete mode 100644 tests/modules/nf-core/bam2fastx/bam2fastq/test.yml

diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test
new file mode 100644
index 00000000000..0d4f80ae699
--- /dev/null
+++ b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test
@@ -0,0 +1,37 @@
+
+nextflow_process {
+
+    name "Test Process BAM2FASTX_BAM2FASTQ"
+    script "../main.nf"
+    process "BAM2FASTX_BAM2FASTQ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bam2fastx"
+    tag "bam2fastx/bam2fastq"
+
+    test("test-bam2fastx-bam2fastq") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/alz.bam.pbi', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap
new file mode 100644
index 00000000000..342241ef940
--- /dev/null
+++ b/modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "test-bam2fastx-bam2fastq": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb"
+                ],
+                "fastq": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.fastq.gz:md5,8abf16176fd1625998ee28590e1039b1"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1b954947255d9b2ad16d2c523258cceb"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T06:30:10.25178642"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 8724459c084..dfc7ff75421 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -34,9 +34,6 @@ atlas/splitmerge:
 authentict/deam2cont:
   - modules/nf-core/authentict/deam2cont/**
   - tests/modules/nf-core/authentict/deam2cont/**
-bam2fastx/bam2fastq:
-  - modules/nf-core/bam2fastx/bam2fastq/**
-  - tests/modules/nf-core/bam2fastx/bam2fastq/**
 bamtools/convert:
   - modules/nf-core/bamtools/convert/**
   - tests/modules/nf-core/bamtools/convert/**
diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf b/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf
deleted file mode 100644
index d8073765b6d..00000000000
--- a/tests/modules/nf-core/bam2fastx/bam2fastq/main.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BAM2FASTX_BAM2FASTQ } from '../../../../../modules/nf-core/bam2fastx/bam2fastq/main.nf'
-
-workflow test_bam2fastx_bam2fastq {
-
-    input = [
-        [ id:'test' ], // meta map
-        file(params.test_data['homo_sapiens']['pacbio']['alz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['pacbio']['alzpbi'], checkIfExists: true)
-    ]
-
-    BAM2FASTX_BAM2FASTQ ( input )
-}
diff --git a/tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config b/tests/modules/nf-core/bam2fastx/bam2fastq/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/bam2fastx/bam2fastq/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/bam2fastx/bam2fastq/test.yml b/tests/modules/nf-core/bam2fastx/bam2fastq/test.yml
deleted file mode 100644
index 18b9f144a72..00000000000
--- a/tests/modules/nf-core/bam2fastx/bam2fastq/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: bam2fastx bam2fastq test_bam2fastx_bam2fastq
-  command: nextflow run ./tests/modules/nf-core/bam2fastx/bam2fastq -entry test_bam2fastx_bam2fastq -c ./tests/config/nextflow.config
-  tags:
-    - bam2fastx/bam2fastq
-    - bam2fastx
-  files:
-    - path: output/bam2fastx/test.fastq.gz
-      md5sum: f0329f9ea12324c6631ac9f3712f2ca5
-    - path: output/bam2fastx/versions.yml