From 82bab9c6e5899818d962994e647f8a46333f9b17 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 2 Jun 2025 18:35:16 +0200 Subject: [PATCH 1/5] handle missing test/nextflow.config gracefully --- nf_core/pipelines/lint/nf_test_content.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nf_core/pipelines/lint/nf_test_content.py b/nf_core/pipelines/lint/nf_test_content.py index 09c3a7147f..5fc8382626 100644 --- a/nf_core/pipelines/lint/nf_test_content.py +++ b/nf_core/pipelines/lint/nf_test_content.py @@ -141,6 +141,10 @@ def nf_test_content(self) -> Dict[str, List[str]]: "description": "`pipelines_testdata_base_path`", }, } + # Check if tests/nextflow.config is present + if not conf_fn.exists(): + failed.append(f"'{conf_fn.relative_to(self.wf_path)}' does not exist") + return {"passed": passed, "failed": failed, "ignored": ignored} if nf_test_content_conf is None or str(conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf: checks_passed = {check: False for check in config_checks} From ea471afd2392a678c846b9806ba5d8427fa48d7e Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 2 Jun 2025 18:37:05 +0200 Subject: [PATCH 2/5] update changelog --- CHANGELOG.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1cacdee501..a39f1d3387 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,19 @@ # nf-core/tools: Changelog +## v3.3.2dev + +### Template + +### Linting + +- Fix linting of nf-test files content ([#3602](https://github.com/nf-core/tools/pull/3602)) + +### Modules + +### Subworkflows + +### General + ## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02] ### Template From 36a417ef0a47c45211ba2c64c09c28ad19cad6db Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 2 Jun 2025 18:37:50 +0200 Subject: [PATCH 3/5] bump version --- .gitpod.yml | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index db31d01bed..d5948695bf 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,4 @@ -image: nfcore/gitpod:latest +image: nfcore/gitpod:dev tasks: - name: install current state of nf-core/tools and setup pre-commit command: | diff --git a/setup.py b/setup.py index cfbcf96d8c..8f4d2fc5dd 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "3.3.1" +version = "3.3.2dev" with open("README.md") as f: readme = f.read() From d182bf7d4136880c053da8b93c48f4e706bfe9d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 5 Jun 2025 12:42:04 +0200 Subject: [PATCH 4/5] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a39f1d3387..d846433a4f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ ### Linting -- Fix linting of nf-test files content ([#3602](https://github.com/nf-core/tools/pull/3602)) +- Fix linting of nf-test files content ([#3603](https://github.com/nf-core/tools/pull/3603)) ### Modules From d3511d1bf08646c6fd64518b40aeb391ac63e9b6 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 5 Jun 2025 12:46:29 +0200 Subject: [PATCH 5/5] remove return --- nf_core/pipelines/lint/nf_test_content.py | 1 - 1 file changed, 1 deletion(-) diff --git a/nf_core/pipelines/lint/nf_test_content.py b/nf_core/pipelines/lint/nf_test_content.py index 5fc8382626..44bd6062cc 100644 --- a/nf_core/pipelines/lint/nf_test_content.py +++ b/nf_core/pipelines/lint/nf_test_content.py @@ -144,7 +144,6 @@ def nf_test_content(self) -> Dict[str, List[str]]: # Check if tests/nextflow.config is present if not conf_fn.exists(): failed.append(f"'{conf_fn.relative_to(self.wf_path)}' does not exist") - return {"passed": passed, "failed": failed, "ignored": ignored} if nf_test_content_conf is None or str(conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf: checks_passed = {check: False for check in config_checks}