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...
View ArticleFirecloud 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....
View ArticleAre 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...
View ArticleIs 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...
View ArticleAny 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?
View ArticleCan'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...
View ArticleBUG: 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...
View ArticleJES 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)....
View ArticleJobs 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...
View ArticleThere 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...
View ArticleRFE: 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...
View ArticleBUG: 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...
View ArticleRFE: 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.
View ArticleNew to firecloud. Where can I see existing pipelines for gene fusion...
For example, STAR-Fusion?
View ArticleBUG: 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.
View ArticleFeature 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...
View Articleis 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...
View ArticleCompleted 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...
View Article502 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...
View Article