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Use correct key for parsing defaultIgnoreParams #3205

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merged 2 commits into from
Oct 9, 2024
Merged

Use correct key for parsing defaultIgnoreParams #3205

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005eaec
use correct key for defaultIgnoreParams
mashehu Oct 9, 2024
bf2c6bb
add more debugging
mashehu Oct 9, 2024
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1 change: 1 addition & 0 deletions nf_core/modules/lint/main_nf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
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3 changes: 2 additions & 1 deletion nf_core/pipelines/schema.py
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Expand Up @@ -97,8 +97,9 @@ 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:
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"
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