Philipp Hahnel

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3. Java Runtime Environment crash in FilterAlignmentArtifacts

Dear Samantha, despite updating the input for the FilterAlignmentArtifacts call, the error unfortunately still persists.  Would the GATK community forum that you linked to a better place to ask for...

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• January 27, 2022 10:57
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3. Java Runtime Environment crash in FilterAlignmentArtifacts

Dear Samantha, thank you very much! I've been updating some legacy code, so it must have slipped my attention that the tool was updated in its usage. Thanks as well for pointing me to the threads! ...

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• January 26, 2022 10:33
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3. Java Runtime Environment crash in FilterAlignmentArtifacts

Hi Samatha, I added the support email to the workspace ( https://app.terra.bio/#workspaces/carterlabtest/PH%20playground ). I hope you still have access to the carterlab group (from previous suppor...

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• Edited January 18, 2022 19:38
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Java Runtime Environment crash in FilterAlignmentArtifacts

I am trying to run FilterAlignmentArtifacts on some Mutect2 output (after filtering etc), however, the Java Runtime Environment crashes. This is also the case for every other gatk docker version th...

• Philipp Hahnel
• January 18, 2022 16:25
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3. scatter over optional array

Hey Jason, I pondered a bit more about it and simplified it to some satisfactory state. I flattened the nested scatter and restricted the none_file hack to the scatter context: version developmentw...

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• January 18, 2022 14:35
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3. scatter over optional array

I realized that if we don't work with Strings but Files, we have to work a bit harder: version developmentworkflow runIterationWithNone { input { Boolean create_inner_array File te...

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• December 14, 2021 06:54
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3. scatter over optional array

All right, a workaround is to replace None with an empty string "" and then deal with the empty string in the task: version developmentworkflow runIterationWithNone { input { Boolean crea...

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• December 13, 2021 22:43
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3. scatter over optional array

Dear Jason, thanks a lot for reaching out to your colleagues! I'd appreciate if your WDL expert would have a closer look at this whenever is convenient. I'll also try other channels and will poke a...

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• December 09, 2021 16:08
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3. scatter over optional array

Thanks, Jason. The ultimate goal is to set up a proper multisample mutect2 pipeline. GATK currently does "multisample" by just running M2 in single tumor-normal pair mode for all pairs ... . Input ...

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• December 07, 2021 20:33
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