[WIP] Command to generate pipeline container config files #3955
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mirpedrol
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mashehu
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Dec 3, 2025
mashehu
reviewed
Dec 3, 2025
Co-authored-by: Matthias Hörtenhuber <[email protected]>
mashehu
reviewed
Dec 4, 2025
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| def __init__( | ||
| self, | ||
| workflow_directory: str | Path = ".", |
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| workflow_directory: str | Path = ".", | |
| workflow_directory: Path = Path("."), |
| workflow_directory: str | Path = ".", | ||
| org: str = "nf-core", | ||
| ): | ||
| self.workflow_directory = Path(workflow_directory) |
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| self.workflow_directory = Path(workflow_directory) | |
| self.workflow_directory = workflow_directory |
| return None | ||
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| def try_generate_container_configs(directory: str | Path, path: str): |
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| def try_generate_container_configs(directory: str | Path, path: str): | |
| def try_generate_container_configs(directory: Path, path: Path): |
let's make this simpler
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| try: | ||
| # Run nextflow inspect | ||
| executable = "nextflow" | ||
| cmd_params = f"inspect -format config {self.workflow_directory}" | ||
| cmd_out = run_cmd(executable, cmd_params) | ||
| if cmd_out is None: | ||
| raise UserWarning("Failed to run `nextflow inspect`. Please check your Nextflow installation.") |
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I have a feeling we have this multiple times in our code base. should this be a utils function?
| try: | ||
| # Run nextflow inspect | ||
| executable = "nextflow" | ||
| cmd_params = f"inspect -format config {self.workflow_directory}" |
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why not -format json would make it easier to parse and we would not need any regex
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so instead of writing the default out first and extracting all info from there, i would hold the config info in a dict and write it out to all configs from there.
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close #3953
Done:
nextflow inspectand obtain docker config filenf-core modules install|update|removeTODO: