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Implement new auto-process 'info' command #895

Merged
merged 7 commits into from
Dec 20, 2023
Merged

Implement new auto-process 'info' command #895

merged 7 commits into from
Dec 20, 2023

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pjbriggs
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@pjbriggs pjbriggs commented Oct 20, 2023

Implements a new info command within auto_process.py, as a lightweight alternative to using the metadata and params commands to get information about the current analysis directory.

Information to include:

  • Run ID
  • Bases mask
  • Flow cell mode
  • Run configuration

(The PR includes updates to the setup command internals, to acquire and store a new run_configuration metadata item which describes the reads and numbers of bases determined from the RunInfo.xml file of the sequencing run (e.g. R1:101bp, I1:8bp, I2:8bp, R2:101bp). The run configuration is generated by a new function get_run_config, in the bcl2fastq/utils module.)

@pjbriggs pjbriggs changed the title WIP implement new auto-process 'info' command Implement new auto-process 'info' command Dec 20, 2023
@pjbriggs pjbriggs removed the WIP Work in progress label Dec 20, 2023
@pjbriggs pjbriggs merged commit 24cd81f into devel Dec 20, 2023
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@pjbriggs pjbriggs deleted the add-info-command branch December 20, 2023 10:26
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