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Add parameters to the nextflow config #3853

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@sofstam sofstam commented Oct 16, 2024

Description

Changed

How to prepare for test

  • Ssh to relevant server (depending on type of change)
  • Use stage: us
  • Paxa the environment: paxa
  • Install on stage (example for Hasta):
    bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b write_config_taxprofiler -a

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  • MAJOR - when you make incompatible API changes
  • MINOR - when you add functionality in a backwards compatible manner
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

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@sofstam sofstam marked this pull request as ready for review November 15, 2024 11:07
@sofstam sofstam requested a review from a team as a code owner November 15, 2024 11:07
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@henrikstranneheim henrikstranneheim left a comment

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Nice cleanup!

@staticmethod
def get_bundle_filenames_path() -> Path:
"""Return Taxprofiler bundle filenames path."""
return TAXPROFILER_BUNDLE_FILENAMES_PATH

@property
def is_params_appended_to_nextflow_config(self) -> bool:
"""Return True if parameters should be added into the nextflow config file instead of the params file."""
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How does it return true?

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sonarcloud bot commented Nov 21, 2024

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