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In some processes, extra java arguments and extra command arguments both point on the same configuration variable ext.args #14

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LysianeBouchard opened this issue Aug 26, 2024 · 0 comments
Open

In some processes, extra java arguments and extra command arguments both point on the same configuration variable ext.args #14

LysianeBouchard opened this issue Aug 26, 2024 · 0 comments
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@LysianeBouchard
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Description of the bug

Consequence is that, if I specify a value for ext.args for those processes, it will appear both in java arguments and main executable arguments.

Processes with this behaviour at the moment moment of writing this doc:

  • importGVCF
  • hardFiltering
  • variantRecalibratorSNP
  • variantRecalibratorIndel
  • applyVQSRSNP
  • applyVQSRIndel

It might be a good idea to visit each local process one by one to double check.

Command used and terminal output

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