From d03b7ae235fd4b7de55b6c26bb57489a9b041399 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Thu, 30 Nov 2023 14:55:56 +0100
Subject: [PATCH] delete component from pytest_modules.yml

---
 nf_core/components/create.py | 11 +++++++++++
 tests/modules/create.py      | 11 +++++++++++
 tests/subworkflows/create.py | 11 +++++++++++
 3 files changed, 33 insertions(+)

diff --git a/nf_core/components/create.py b/nf_core/components/create.py
index 70fcfb21a0..b85acdc57f 100644
--- a/nf_core/components/create.py
+++ b/nf_core/components/create.py
@@ -17,11 +17,13 @@
 import jinja2
 import questionary
 import rich
+import yaml
 from packaging.version import parse as parse_version
 
 import nf_core
 import nf_core.utils
 from nf_core.components.components_command import ComponentCommand
+from nf_core.lint_utils import run_prettier_on_file
 
 log = logging.getLogger(__name__)
 
@@ -475,3 +477,12 @@ def _print_and_delete_pytest_files(self):
                 "You can find more information about nf-test [link=https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test]at the nf-core web[/link].\n"
                 f"Once done, make sure to delete the module pytest files to avoid linting errors: {pytest_dir}"
             )
+        # Delete tags from pytest_modules.yml
+        modules_yml = Path(self.directory, "tests", "config", "pytest_modules.yml")
+        with open(modules_yml, "r") as fh:
+            yml_file = yaml.safe_load(fh)
+        yml_key = self.component_dir if self.component_type == "modules" else f"subworkflows/{self.component_dir}"
+        del yml_file[yml_key]
+        with open(modules_yml, "w") as fh:
+            yaml.dump(yml_file, fh)
+        run_prettier_on_file(modules_yml)
diff --git a/tests/modules/create.py b/tests/modules/create.py
index 062761d059..9c855a11e6 100644
--- a/tests/modules/create.py
+++ b/tests/modules/create.py
@@ -7,6 +7,7 @@
 import pytest
 import requests_cache
 import responses
+import yaml
 from git.repo import Repo
 
 import nf_core.modules
@@ -105,6 +106,11 @@ def test_modules_migrate(self, mock_rich_ask):
     # Check that pytest folder is deleted
     assert not pytest_dir.is_dir()
 
+    # Check that pytest_modules.yml is updated
+    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+        modules_yml = yaml.safe_load(fh)
+    assert "samtools/sort" not in modules_yml.keys()
+
 
 @mock.patch("rich.prompt.Confirm.ask")
 def test_modules_migrate_no_delete(self, mock_rich_ask):
@@ -123,3 +129,8 @@ def test_modules_migrate_no_delete(self, mock_rich_ask):
 
     # Check that pytest folder is not deleted
     assert pytest_dir.is_dir()
+
+    # Check that pytest_modules.yml is updated
+    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+        modules_yml = yaml.safe_load(fh)
+    assert "samtools/sort" not in modules_yml.keys()
diff --git a/tests/subworkflows/create.py b/tests/subworkflows/create.py
index 88f98b9453..2855e68e2c 100644
--- a/tests/subworkflows/create.py
+++ b/tests/subworkflows/create.py
@@ -5,6 +5,7 @@
 from unittest import mock
 
 import pytest
+import yaml
 from git.repo import Repo
 
 import nf_core.subworkflows
@@ -75,6 +76,11 @@ def test_subworkflows_migrate(self, mock_rich_ask):
     # Check that pytest folder is deleted
     assert not pytest_dir.is_dir()
 
+    # Check that pytest_modules.yml is updated
+    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+        modules_yml = yaml.safe_load(fh)
+    assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()
+
 
 @mock.patch("rich.prompt.Confirm.ask")
 def test_subworkflows_migrate_no_delete(self, mock_rich_ask):
@@ -95,3 +101,8 @@ def test_subworkflows_migrate_no_delete(self, mock_rich_ask):
 
     # Check that pytest folder is not deleted
     assert pytest_dir.is_dir()
+
+    # Check that pytest_modules.yml is updated
+    with open(Path(self.nfcore_modules, "tests", "config", "pytest_modules.yml")) as fh:
+        modules_yml = yaml.safe_load(fh)
+    assert "subworkflows/bam_stats_samtools" not in modules_yml.keys()