Importing a task (with no workflow) into a workspace results in a misleading...
http://imgur.com/a/yQauM The message should probably say something to the effect of "cannot import tasks into workspaces. Please use workflows only."
View ArticleFailure cloning a workspace
I attempted to clone a workspace that has a user-defined Authorization Domain attached to it, and in which a number of analyses have been run. I get a failure report. See attached screenshots.
View ArticleUsing quotes in method configuration strings?
Hi, I'm wondering how Firecloud handles quotes in the Input string attribute in method configurations. Within a string, I'd like to add quotes to pass on to my method. In bash, the symbol \" has done...
View ArticleVersioning of method configuration
This may have been asked before, but I can't find the relevant thread... It looks like any change to a method configuration automatically triggers a version increase. It would be very useful to be able...
View Articleare workflows in a submission scattered uniform across cromwells? impact to CC?
If I issue a submission in FC with a pair-set (or any set) with N elements in the set so that N workflows are launched in the submission, are the workflows expected to be run on the various cromwell...
View ArticleWhere did the broadinstitute/firecloud-cli github repo go?
We use the firecloud-cli for some of our automation tools. We can no longer find the repo on github. (firecloud-cli was one of firecloud's public facing user interfaces...you shouldn't eliminate it...
View ArticleCan we have an option to disable email notifications?
Hi Firecloud Team, Would it be possible to set a checkbox somewhere to not send notifications when workspaces are shared with me? I don't want to filter all emails from firecloud, but I also don't want...
View ArticleRunning but no operations ID?
I have a job that has been "Running" for about 10 minutes now. However, there is NO operations ID. I did some network tab inspection and found no useful information. Workflow...
View Articleempty events array after 20 minutes?
A task is "Running" on FC for over 30 minutes: QC_Workflow.QC_Prepare_TaskHide Call #1: ID:operations/EL3xgcK2Kxjru7rUwM6jwzEgt5KztIUCKg9wcm9kdWN0aW9uUXVldWU Status: Running Cache Result:Miss...
View ArticleFireCloud exceedingly slow since this morning
It takes about 30 minutes to get an operations ID for a single-task workflow. Could this be related to the new release?
View Articlefiltering a trio joint VCF based on GT DP
Hi I have a joint VCF with a trio of samples in it, and would like to only retain those sites where all 3 samples have at least DP >=10 in their respective GT FORMAT field. I have been trying to do...
View Articleis the call-cache cache ever cleared?
Was it cleared during the recent FC upgrade? -eddie
View ArticleAuthorization Domains no longer being displayed in Workspace summary page
I created an Authorization Domain (Realm) a couple of weeks ago for an industry collaboration and we created a number of workspaces under that Authorization Domain. With the new release of FireCloud,...
View ArticleQueued, but not Queued
I have a task (call #8 in a scatter): Call #8: ID: Status: QueuedInCromwell Cache Result:Miss Started:April 13, 2017, 2:34 PM (20 hours ago) Ended:Pending... Inputs:None Outputs:None stdout: stderr: As...
View Articleover an hour to check the call-cache?
I made a submission earlier today. The first task "sizesCalc" was a "Hit" from the cache, but it took over an hour to do the cache-lookup according to the timing diagram (see attachment). Workflow...
View Articlefeature request : "Show All"? and "Hide All"? or show-failed by default?
for calls in a workflow, in the UI, each is under a "show/hide" status in the UI. Furthermore, under each call, the inputs and outputs are also under a "show/hide" If a task is marked "Failed" I think...
View ArticleAuthorization Domains no longer being displayed in Workspace summary page
I created an Authorization Domain (Realm) a couple of weeks ago for an industry collaboration and we created a number of workspaces under that Authorization Domain. With the new release of FireCloud,...
View ArticleDeleting attributes (API)
The 'delete' API call (https://api.firecloud.org/#!/Entities/deleteEntities) only allows for deletion of an entire entity. It would be very convenient to be able to delete a specific attribute (either...
View Article[warn] Localization via hard link has failed Invalid cross-device link
Ηello, I'm trying to run GATK best practices and I've run in to a wall when the SamToFastqAndBwaMem is executed. First things first: in the .inputs.json I specified my .fa.alt via absolute path and I...
View ArticleFailed to upload authentication file
I made submission f4e7a548-76b7-4303-88ab-1816b1098330 today on FC. The submission was on a pair set with 1080 pairs. Of the 1080 pairs, exactly 8 failed with the following message (observed by...
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