
Stephanie Gogarten
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Latest activity by Stephanie Gogarten
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Stephanie Gogarten commented,
Thanks Ash! I feel like the bigger issue here is a failure of Dockstore search, because even knowing that the exact workflow I want exists, it's not straightforward to find it. I posted about this ...
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Stephanie Gogarten commented,
Is there now a readily available WDL to run `samtools index`? I tried searching for one on dockstore, but got >200 results for WDLs that contain indexing somewhere as a step. I also tried searching...
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Stephanie Gogarten created a post,
Workflow succeeded despite error code
I am writing a workflow that contains a series of commands in the command block. If the final command returns an error code, the workflow fails, but if an earlier command in the series returns an e...
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Stephanie Gogarten created a post,
Size limits on data tables?
We are trying to create very large data tables in a workspace to track simulated genotype data. We are using the Bioconductor::AnVIL R functions avtable_import and avtable_import_set to write to th...
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Stephanie Gogarten created a post,
Latest 1000G VCF files on AnVIL?
Are the most recent VCF files from the high-coverage 1000 Genomes dataset available on AnVIL, or are there plans to make them available soon? The 1000 Genomes public workspace only has the much old...
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Stephanie Gogarten commented,
Is it possible to preserve the ordering in the initial TSV file (or Python/R table when interacting with data tables programmatically)? Our project will be creating hundreds of workspaces, so chang...
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Stephanie Gogarten commented,
Interesting, when I click on the file (which has a DRS identifier), I get a curl command to download instead of gsutil. So maybe this is a known limitation of gsutil for controlled access data; it ...
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Stephanie Gogarten commented,
I just tried again after several days and got the same error: gsutil -u terra-c9b4d853 cp gs://nih-nhlbi-topmed-released-phs000964-c3/phs000964.v3.pht004839.v2.p1.TOPMed_WGS_JHS_Sample.MULTI.txt.gz...
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Stephanie Gogarten commented,
I have linked my NIH account, as well as my account with NHLBI BioData Catalyst Framework Services, which is what gives me access to this particular file via its DRS and terra-notebook-utils. I jus...
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Stephanie Gogarten commented,
My account is not a user on the google billing project, so that must be the problem for the first part of this question. A subset of our team manages Google billing, and we create new workspaces un...
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