Stephanie Gogarten

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2. General Discussion
3. How to index a CRAM file on Terra with samtools?

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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• Edited August 30, 2023 22:09
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1. Community
2. General Discussion
3. How to index a CRAM file on Terra with samtools?

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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• August 29, 2023 23:00
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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...

• Stephanie Gogarten
• Edited June 01, 2023 22:56
• 2 followers
• 1 comment
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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...

• Stephanie Gogarten
• April 03, 2023 18:47
• 2 followers
• 1 comment
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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...

• Stephanie Gogarten
• February 11, 2023 00:06
• 2 followers
• 1 comment
• 0 votes

1. Community
2. Completed Feature Requests
3. Set metadata column order during tsv upload

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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• February 10, 2023 23:18
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2. General Discussion
3. Error "Permission 'storage.buckets.list' denied on resource" when using gsutil

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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• February 01, 2023 19:40
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2. General Discussion
3. Error "Permission 'storage.buckets.list' denied on resource" when using gsutil

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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• January 31, 2023 21:33
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1. Community
2. General Discussion
3. Error "Permission 'storage.buckets.list' denied on resource" when using gsutil

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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• January 26, 2023 17:37
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