Please update the temp-dir parameter in the docs

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Giovanni A Crestani

• September 19, 2024 19:25
• Edited

Hello! I am writing commands for a pipeline that uses GATK, and I need to specify the temporary directory so things work in my cluster. The documentation page (example) of most tools I use tells me that the parameter to define a temporary directory is `--TMP_DIR`. However, I discovered that it is `--tmp-dir` now. I would suggest you update the documentation!

Giovanni

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  Gökalp Çelik

  • September 19, 2024 22:30
  • Edited

  Hi Giovanni A Crestani

  The version that you are looking at is 4.0.0.0 which is quite old and currently unsupported. Latest version of GATK and documentation indicates the correct parameter for designating temporary folder for each tool. 

  https://gatk.broadinstitute.org/hc/en-us/articles/27007944031643--Tool-Documentation-Index 

  We also have a writing about how to setup temporary folder for GATK and related tools in the link below. Shortly tools that are coming from picard use --TMP_DIR parameter whereas tools that are genuinely in GATK use --tmp-dir. There is also an alternative way of setting temporary directory through direct java parameters which is the same for both picard tools in GATK and genuine GATK  tools.

  https://gatk.broadinstitute.org/hc/en-us/articles/18965297287067-How-to-setup-and-use-temporary-folder-for-GATK-local-execution 

  I hope this helps.

  Regards.  

   

   

   

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  Giovanni A Crestani

  • September 20, 2024 00:07

  Amazing! I was unaware I was using an older version. Thank you for pointing that out!

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