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FISS within a wdl task - Application Default Credentials

Hi- I have a wdl task that uses FISS python bindings to access the workspace data model. While this works fine locally, I receive a credential error when running in Firecloud: Traceback (most recent...

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Firecloud not correctly reporting status of jobs run on Sample Sets

Hello, I ran the same method configuration on two different sample sets in their respective workspaces, and if I view the status of the job, it will show it is done, as in the attached screenshot....

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Are there working examples of a WDL that import a WDL from a URL ?

Somewhat inspired by the 15 November announcement that FireCloud's Method Repository now supports WDLs with HTTP imports referencing the URL of other public methods in the FC repository, I attempted to...

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Is there a way to search the methods repo for examples of syntax ?

Is there a way to search the methods repo for examples of syntax? For example, someone might want to a search for examples of WDL's that import methods from a URL. The existing search tool on the...

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Feedback

Is there a place to provide feedback on GATK tools and help text?

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Any way (or plan) ro launch WDL in FireCloud without creating workspace?

Is there a way, or a plan to privide a way, to launch certain WDL script against certain data via calling Firecloud API, and withoud a need to create workspace?

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Can't register for Firecloud

I tried to make a FireCloud account But it wouldn't let me login - I have seen this happen before with the ORSP portal. And they told me that it just doesn't work with Chrome on a PC. I guess this is...

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BUG: loading multiple set entities via the importEntities API returns a 502...

This has been noted by myself, @smeier, and @francois_a. When using the importEntity API with a tsv file containing multiple set entities, we often get a return code of 502, however when we look at the...

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JES error code 2. Message: Instance failed to start due to preemption

Seeing multiple instances of this (for example, workflow 2bd68c76-d225-4cc8-a226-e5eb28c48474, submission 20b7af64-5a22-4c4b-8b19-e8b03de85880; I've added GROUP_support@firecloud.org to the workspace)....

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Jobs that take unusually long times

Hi I've got a workflow that was run on a pair_set with 86 pairs. 84 of the pairs finished within a few hours but 2 pairs have been processing for more than 3 days (workflow ids...

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There are no rows to display.

Workspace firehose-to-firecloud/REBC_Chanock_NCI is a data delivery workspace that has 902 WGS bams from 342 patients. When viewing the Data / sample (902 total) tab there is a message " There are no...

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RFE: Return memory usage stats

It would be amazing if we could get back how much memory our tools use in FireCloud. Because a lot of what is run on FC is too big or cumbersome to run locally, pre-FC memory profiling can be hit or...

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BUG: If a method is edited in a workspace with no data, Root Entity Type is...

If a workspace is populated with method configs, but contains no data, editing a method config in the workspace will clear its Root Entity Type, with no way to change it back (other than presumably...

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RFE: allow setting of attribute type via API

There does not seem to be a way to set an attribute type as Boolean via the API; if a workspace attribute is created and set to true or false via the API, the type ends up being String.

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New to firecloud. Where can I see existing pipelines for gene fusion...

For example, STAR-Fusion?

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BUG: GUI reporting no entity attributes defined when there are entity attributes

I ran into this while looking at the pairs table. I clicked on one of the pairs for which entity attributes were definintely defined, but the system reported not entity attributes.

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Feature Req: support for requestor-pays buckets for gcr.io-based docker...

I have some docker images I want to store on Google Cloud Repository (gcr.io). There is no IP precluding public access, so I don't need to jump through the hoops that would otherwise be required to...

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is column deletion possible?

It is my understanding that currently in FC workspaces that it is NOT possible to delete a column for a data entity. For example, if you have a sample for a participant and a column for that sample...

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Completed workflows marked as "Running"; outputs not written to data model

Hundreds of my jobs are currently in this state. Many finished running hours ago. Under "Monitor", the status is marked a successful, and the output from the...

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502 Server Error on submission

This may be related to https://gatkforums.broadinstitute.org/firecloud/discussion/10854/bug-loading-multiple-set-entities-via-the-importentities-api-returns-a-502-error-code but unlike that issue, the...

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