From b47e98406387c035789f5dfc4f318f354304123f Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Mon, 26 Aug 2024 09:24:23 +1200
Subject: [PATCH] Added nf-test for picard/sortsam

---
 .../nf-core/picard/sortsam/tests/main.nf.test | 40 +++++++++++++++++++
 .../picard/sortsam/tests/main.nf.test.snap    | 15 +++++++
 .../picard/sortsam/tests/nextflow.config      |  5 +++
 tests/config/pytest_modules.yml               |  3 --
 tests/modules/nf-core/picard/sortsam/main.nf  | 14 -------
 .../nf-core/picard/sortsam/nextflow.config    |  9 -----
 tests/modules/nf-core/picard/sortsam/test.yml |  9 -----
 7 files changed, 60 insertions(+), 35 deletions(-)
 create mode 100644 modules/nf-core/picard/sortsam/tests/main.nf.test
 create mode 100644 modules/nf-core/picard/sortsam/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/picard/sortsam/tests/nextflow.config
 delete mode 100644 tests/modules/nf-core/picard/sortsam/main.nf
 delete mode 100644 tests/modules/nf-core/picard/sortsam/nextflow.config
 delete mode 100644 tests/modules/nf-core/picard/sortsam/test.yml

diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test b/modules/nf-core/picard/sortsam/tests/main.nf.test
new file mode 100644
index 00000000000..9d9af09ea77
--- /dev/null
+++ b/modules/nf-core/picard/sortsam/tests/main.nf.test
@@ -0,0 +1,40 @@
+
+nextflow_process {
+
+    name "Test Process PICARD_SORTSAM"
+    script "../main.nf"
+    process "PICARD_SORTSAM"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "picard"
+    tag "picard/sortsam"
+
+    test("test-picard-sortsam") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
+                ]
+				input[1] = "queryname"
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test.snap b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap
new file mode 100644
index 00000000000..bf447b8d135
--- /dev/null
+++ b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap
@@ -0,0 +1,15 @@
+{
+    "test-picard-sortsam": {
+        "content": [
+            "b9847fed94d2b7286e18caaa099658ce",
+            [
+                "versions.yml:md5,f53876b7c58b5aa1564606f3c9c34108"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-26T09:23:48.485054"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/picard/sortsam/tests/nextflow.config b/modules/nf-core/picard/sortsam/tests/nextflow.config
new file mode 100644
index 00000000000..8512101e96f
--- /dev/null
+++ b/modules/nf-core/picard/sortsam/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: PICARD_SORTSAM {
+        ext.prefix = { "${meta.id}.sorted" }
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4aea9c2af1e..0358161bd39 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1073,9 +1073,6 @@ picard/renamesampleinvcf:
 picard/scatterintervalsbyns:
   - modules/nf-core/picard/scatterintervalsbyns/**
   - tests/modules/nf-core/picard/scatterintervalsbyns/**
-picard/sortsam:
-  - modules/nf-core/picard/sortsam/**
-  - tests/modules/nf-core/picard/sortsam/**
 picard/sortvcf:
   - modules/nf-core/picard/sortvcf/**
   - tests/modules/nf-core/picard/sortvcf/**
diff --git a/tests/modules/nf-core/picard/sortsam/main.nf b/tests/modules/nf-core/picard/sortsam/main.nf
deleted file mode 100644
index 4b4e801355a..00000000000
--- a/tests/modules/nf-core/picard/sortsam/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PICARD_SORTSAM } from '../../../../../modules/nf-core/picard/sortsam/main.nf'
-
-workflow test_picard_sortsam {
-
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
-    sort_order = "queryname"
-
-    PICARD_SORTSAM ( input, sort_order )
-}
diff --git a/tests/modules/nf-core/picard/sortsam/nextflow.config b/tests/modules/nf-core/picard/sortsam/nextflow.config
deleted file mode 100644
index ca572c2f41c..00000000000
--- a/tests/modules/nf-core/picard/sortsam/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: PICARD_SORTSAM {
-        ext.prefix = { "${meta.id}.sorted" }
-    }
-
-}
diff --git a/tests/modules/nf-core/picard/sortsam/test.yml b/tests/modules/nf-core/picard/sortsam/test.yml
deleted file mode 100644
index 9322ed77b5b..00000000000
--- a/tests/modules/nf-core/picard/sortsam/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: picard sortsam test_picard_sortsam
-  command: nextflow run ./tests/modules/nf-core/picard/sortsam -entry test_picard_sortsam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/sortsam/nextflow.config
-  tags:
-    - picard
-    - picard/sortsam
-  files:
-    - path: output/picard/test.sorted.bam
-      md5sum: b44a6ca04811a9470c7813c3c9465fd5
-    - path: output/picard/versions.yml