Philipp Hahnel
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Recent activity by Philipp Hahnel
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Just as a follow-up note for importing arrays in TSVs: https://support.terra.bio/hc/en-us/community/posts/4405453406235/comments/4410978206363 Documenting that they need to be JSON-valid is also he...
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> Note that TSV functions in the Data tab does not currently work for sets of sets. It would be helpful to note this in the documentation. How is this currently supposed to be handled? I have a job...
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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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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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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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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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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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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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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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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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