Feature/nucleovar operator #1365
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buehlere
commented
Oct 4, 2024
•
buehlere
commented
- Adding nextflow operator for nucleovar pipeline
- option to create input json from nf-core schemas
- passing nfcore template parameter to ridgeback
adding the ability to specify an app
sivkovic
reviewed
Oct 24, 2024
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| class NextflowRunObject(RunObject): | ||
| logger = logging.getLogger(__name__) | ||
| # logger = logging.getLogger(__name__) |
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We can probably remove this if it is not used anywhere
sivkovic
reviewed
Oct 24, 2024
runner/pipeline/pipeline_cache.py
Outdated
| @@ -16,7 +16,7 @@ def get_pipeline(pipeline): | |||
| resolved_dict = _pipeline.get("app") | |||
| else: | |||
| resolver_class = PipelineCache._get_pipeline_resolver(pipeline.pipeline_type) | |||
| resolver = resolver_class(pipeline.github, pipeline.entrypoint, pipeline.version) | |||
| resolver = resolver_class(pipeline.github, pipeline.entrypoint, pipeline.nfcore_template, pipeline.version) | |||
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Can you re-order params so nfcore_template is last one and put nfcore_template as param with default value, since I am not sure this will work for CWL pipelines.
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