From 005eaec876469ad37834c1b180eba8b8147039e8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 9 Oct 2024 10:12:06 +0200 Subject: [PATCH 1/2] use correct key for defaultIgnoreParams --- nf_core/pipelines/schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 3aec815c7..37ba4feaf 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -97,7 +97,7 @@ def _update_validation_plugin_from_config(self) -> None: conf.get("validation.help.fullParameter", "helpFull"), conf.get("validation.help.showHiddenParameter", "showHidden"), ] # Help parameter should be ignored by default - ignored_params_config = conf.get("validation", {}).get("defaultIgnoreParams", []) + ignored_params_config = conf.get("validation.defaultIgnoreParams", []) if len(ignored_params_config) > 0: ignored_params.extend(ignored_params_config) self.ignored_params = ignored_params From bf2c6bb7169afb040630c387bac0a1036fec9b77 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 9 Oct 2024 10:12:23 +0200 Subject: [PATCH 2/2] add more debugging --- nf_core/modules/lint/main_nf.py | 1 + nf_core/pipelines/schema.py | 1 + 2 files changed, 2 insertions(+) diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py index dbc1bed73..54a69b113 100644 --- a/nf_core/modules/lint/main_nf.py +++ b/nf_core/modules/lint/main_nf.py @@ -342,6 +342,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar): continue try: container_url = "https://" + urlunparse(url) if not url.scheme == "https" else urlunparse(url) + log.debug(f"Trying to connect to URL: {container_url}") response = requests.head( container_url, stream=True, diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 37ba4feaf..1f0b4d5e3 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -99,6 +99,7 @@ def _update_validation_plugin_from_config(self) -> None: ] # Help parameter should be ignored by default ignored_params_config = conf.get("validation.defaultIgnoreParams", []) if len(ignored_params_config) > 0: + log.debug(f"Ignoring parameters from config: {ignored_params_config}") ignored_params.extend(ignored_params_config) self.ignored_params = ignored_params self.schema_draft = "https://json-schema.org/draft/2020-12/schema"