Javascript Error When Clicking on Samples Tab
Hi FC Team, I'm seeing the following error when clicking on the samples tab in my workspace: "A JavaScript error occurred; please try reloading the page. If the error persists, please report it to our...
View Articleminor bug - need to refresh in order to see uploaded workspace attributes
I create a new workspace, and then upload a TSV file that contains workspace attirbutes. The upload is successful, but no workspace attributes are visible. I need to refresh the page in order to see...
View ArticleHas the user interface under "Monitor" changed recently?
Hello, It used to be (if I remember correctly) that I could monitor the progress of a method by selecting on the date (screenshot provided). Has this feature been removed, and is there a way to get...
View ArticleTasks stuck in QueuedInCromwell state (within workflow)
I'm running a workflow consisting of multiple, initially sequential tasks. After the first task completed successfully, the second task got stuck in QueuedInCromwell state (for 21 hours now). The...
View ArticleSubmissions stuck in 'Aborting' state
If there is an error in the runtime block of a WDL, jobs get stuck in 'submitted' state. I tried to terminate these, but they're now stuck in the 'aborting' state instead. Example workflow ID:...
View ArticleClik here to view.
No workflow details to click
I am trying to see the inputs/workflow etc in a workspace I was working on some time ago. I am unable to go into the submission id to see the timing diagram etc: When I click the link on the right it...
View ArticleForeign key links are empty in GUI view of sample and pair tables.
The most recent release appears to have broken the table display. If you go to any of the TCGA cohort workspaces you can see this. For example, in the samples table the participants field is empty, and...
View ArticleMethod Namespaces: docs do not make clear that namespaces are implicitly created
Today I tried to help a new user create a new namespace in the method repository. But after searching the docs and forum several times, I could not locate a snippet of documentation that addresses this...
View ArticleRerun workflows in failed or aborted state
This is a feature request. Consider the following usage scenario: I launch an analysis on a collection of 1000 samples. 900 of them succeed, but 100 of them get stuck. I abort the submission, but want...
View ArticleAccessing the samples of a participant
It currently isn't possible to access a participant's sample attributes directly, using this.samples.<attribute> This is a significant limitation for analyses across samples (e.g., tissues, cell...
View Articlecom.google.cloud.storage.StorageException: 500 Internal Server Error Backend...
is this a transient error??? see attached -eddie
View ArticleArbitrary sorting of inputs in method configuration?
I'm configuring my new method called DellyForGermlineSV in the broad-firecloud-dsde-methods/CCDG-500-testForManta workspace. The inputs are listed in some order than isn't the order in my WDL and isn't...
View ArticleUnusually long submission delay
Normally when I make a submission, I see the operations id show up within seconds, and after 5 minutes I see the first snapshot of the logs. Currently things are taking much longer - for workflow id:...
View Articletask config name mangling in monitor tab
When I launch a task config, its name shows up in the monitor tab. If I later modify the task config (eg update the wdl snapshot or edit the fields), all previously launched task configs now show up...
View Articlealternative to controlled access...
Hi FireCloud team, I am working on setting up a Mutect analysis pipeline using the BestPractice workspaces as very useful templates. I do not need TCGA data access for my project. I see that currently...
View ArticleExtended Memory?
Hi Firecloud Team, Most of my tasks need way more ram than 6.5GB/cpu, and I would like to use the extended memory feature of GCP to reduce cost....
View ArticleScala error on running new task
What does this error mean? There is no stderr or stdout the only error I can find is from the log: 2017-06-06 17:36:09,014 INFO - MaterializeWorkflowDescriptorActor [UUID(000771a9)]: Call-to-Backend...
View Articlebehavior of workspace attributes downloading
I have a workspace broad-firecloud-eddie/eddie_test_contam_Broad_MutationCalling_QC_Workflow_BestPractice_copy_copy_explore_wsattr I download the workspace attributes (by clicking "Download...
View Articleworkspace attributes list of integers?
I try to set a list of integers in the workspace attributes (see figure attached) but when I try to save the key/value pair as shown in the figure I get an error message : Invalid number for key(s):...
View Articleadditional observation of Unusually long submission delay
This post is related to : http://gatkforums.broadinstitute.org/firecloud/discussion/9675/unusually-long-submission-delay#latest Today, I seem to be observing delays (like those from the...
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