right workflow but wrong data entity?
I made submission today in FC ( f4e7a548-76b7-4303-88ab-1816b1098330). It is on a pair-set. In the monitor tab, I see the workflows for each pair in the pair set. (see wf_listing.png). Note that in the...
View ArticleI can no longer retrieve FireCloud usage statistics.
@abaumann and David Bernick understand the context I can no longer access the usage statistics I need for creating monthly reports. I lost access once I reset the application-default credentials, as...
View ArticleProblem installing fiss for firecloud
Hi, I'm trying to install fiss for firecloud on my local computer, and I'm getting the following error (downloaded the source from github repo): WMBB1-789:fiss-master chrislo$ sudo python setup.py...
View Articleglob output fails when directories are different but file name is the same?
see the WDL: task globber { command <<< set -x mkdir -pv d1 d2 echo "this is one" > d1/out.txt echo "this is two" > d2/out.txt head */out.txt >>> output { Array[File]...
View ArticleQueuedInCromwell for 5 days?
I ran a submission nearly a week ago and a task is queued in cromwell 5 days. every other task seemed to run with no issue. see attached PDF did this task get "forgotten"? -eddie
View Articleno pipeline events after 5 days?
A task was started in FC several days ago : QC_Workflow.ContEST_TaskHide Call #1: ID:operations/EI6mhsa2KxiQjquf1-KGn-IBILeSs7SFAioPcHJvZHVjdGlvblF1ZXVl Status: Running Cache Result:Miss Started:April...
View Articleworkflow was done but has status "running"
Hello. I laucned a same pipeline twice. The both pipeline were successfully done, and I can see their results and a result of final task, but they have status "running" till now. All tasks also have...
View ArticleHow to download specific files from job in batch
Hi FireCloud team, Just ran Polysolver and want to download only the winners.hla.txt specific files from each patient in my cohort (don't want the fees from downloading all other output files). Is...
View ArticleImage preview is slow and prevents opening the image
When there are .png files in the data section of a workspace, clicking on it pulls up a "preview" of the file which looks like the attached screenshot. Unfortunately generating this preview takes a...
View ArticleDocumentation for uploading data
It used to be that when you went to upload a data file there would be a link to documentation (see attached screenshot). The user guide link used to take you to documentation about how to upload data...
View Articlebroken link in shared workspace email?
I heard from @abaumann that FC has new links... I got a workspace shared with me and I got an email as here: FireCloud: kslowik@broadinstitute.org has shared the workspace:...
View ArticleView samples in pair set in sample tab
It seems there should be functionality to subset the data in your 'sample' or 'pairs' tab by members of your various defined sample sets or pair sets. Functionality like this used to exist in firehose...
View ArticleMethod permissions do not propagate across snapshots
Hi, I'd like to make a request for change in FireCloud behavior when updating WDLs. Currently, a firecloud -u https://api.firecloud.org/api -m push ... destroys any app permissions previously granted....
View ArticleSeveral Problems I've noticed in the WDL documentation
*All these issues were encountered while reading the spec file on the WDL github repo. There are some features that are listed as "cromwell supported", but aren't actually supported by the version of...
View ArticleProblem with deleting and recreating workspaces on FireCloud
I created a workspace, let's call it workspace_a. Then I loaded all the info into that workspace from load files that had 6 attributes. Three of those attributes had no data and were filled with...
View ArticleWill FireCloud ever support CWL
Is it planned to support CWL in FireCloud in the future? If not, why not?
View ArticleIs that possible to run analyses on 1000 Genomes dataset using Firecloud?
Hi, Firecloud Team. I've been used Firecloud to analyse TCGA dataset. I'm wondering if it's possible to run the 1000 Genomes dataset using Firecloud? Such as...
View ArticleError sharing workspace
Hello! I just created a new workspace: Workspace: broad-firecloud-ibmwatson/IBM_Q2_Samples_MuTect_Analysis and went to share it with Eddie Salinas and Megan Hanna. I received an error message, which I...
View ArticlelistMethod api calsl should have a namespace parameter
It would be useful if the API call https://api.firecloud.org/#!/Method_Repository/listMethodRepositoryMethods https://api.firecloud.org/#!/Method_Repository/listMethodRepositoryConfigurations accepted...
View ArticleCan Windows binaries be run via FireCloud and/or its Cromwell/JES/GCE...
I'm nearly certain that the answer to this remains "No," but as due diligence I need to ask anyway: is there a way one can tag containers or tasks to target their execution to a Windows VM on the...
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