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Catch Errors and continue in clean FASTQ command #3817

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Vince-janv opened this issue Oct 7, 2024 · 1 comment · May be fixed by #4206
Open
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Catch Errors and continue in clean FASTQ command #3817

Vince-janv opened this issue Oct 7, 2024 · 1 comment · May be fixed by #4206
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@diitaz93

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@Vince-janv
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As a system-administrator,
I want the cleaning of FASTQ files to not stop is something goes wrong with a file,
So that one file does not block the cleaning of 100 000 others.

Work impact

Answer the following questions:

  • Is there currently a workaround for this issue? If so, what is it?
    • Yes, regularly look at the logs of the service and unclog it everytime it gets stuck
  • How much time would be saved by implementing this feature on a weekly basis?
    • ~10 h on yearly basis
  • How many users are affected by this issue?
    • sys-adm and production
  • Are customers affected by this issue?
    • No

Acceptance Criteria

  • One file failing does not block other files from being deleted
    ...

Notes

  • Additional information.
  • Dependencies.
  • Related user stories.
@diitaz93
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Technical refinement

The cleaning of fastq files is called here. We should implement error handling to continue the cleaning when one case fails. Also log properly the errors

@diitaz93 diitaz93 self-assigned this Feb 12, 2025
@diitaz93 diitaz93 linked a pull request Feb 14, 2025 that will close this issue
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add error handling to fastq clean Clinical-Genomics/cg
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@diitaz93 @Vince-janv