Small, simple UI improvements for data tab
In the Data tab: 1) Add a first/last button to the pagination, not just a next/previous (often I'm in the middle of my samples and can't scroll back to the beginning) 2) When sorting, I catch myself...
View ArticleLack of Error Message
Hello! I was attempting to import methods into a workspace and had issues with one of them. When I tried to import a particular method from another workspace, I did not have an "import" button after I...
View ArticleUnable to scatter-gather over entities in firecloud
Hello, I'm working on a pipeline to analyze methylation data. I have it configured to scatter over a set of participants and then gather the result into one result file for the participant set. This...
View ArticleWarning: Creating VM and disk(s) would exceed \"CPUS\" in region us-central1,...
I ran a WDL. The WDL has a scatter in it. One of the scatters had the error message : Warning: Creating VM and disk(s) would exceed \"CPUS\" in region us-central1, will try again I found the message in...
View ArticleRequests to firecloud timing out?
I am trying to list using the API all the samples in a workspace and it seems like it cannot handle large pair sets. amaro@smod-instance:~/Projects/amaro_scratch/SMOD$ fissfc sample_list -w...
View Articlefirecould "loading auth" forever?
I'm getting "Loading auth..." message on every page in firecloud. Not sure how to fix this problem.
View ArticleTCGA Alignment
Hello, In the TCGA controlled access workspaces, what genome are the BAMs aligned to? I see some specific workspaces with hg38. Are there any current tools compatible with hg38 in FireCloud? Thanks,...
View Articleblank fields after cancelling editing a method config
If I go to a workspace and then select any method config (which has its fields filled out) then hit "Edit Configuration" and then (without editing anything) I hit "Cancel Editing" I then see all the...
View ArticleIssues with building a workspace from a billing project
Hello, I received a billing project "nci-mleventh-bi-org" on Firecloud, but when I go to make a workspace, it says that I am not authorized to create a workspace with this billing project....
View Articletask config 'eval' based on specific entity
Firehose had a feature where you could give a specific instance of an entity to a task config, and it would show you how all the attributes resolved. I need to do the same thing in Firecloud. My use...
View ArticleJob stuck in "aborting" state
I have been running a job in the workspace broad-firecloud-methylation/Methylation_Pipeline which was in the "running" state according to firecloud for several days. I tried aborting it on Wednesday...
View ArticleIs there a "null" value that can be used in WDL? Could "else" statements be...
Say I have a task that has different behavior depending on the setting of optional parameters. Is there a null or undefined value in WDL that will cause the defined function to evaluate to false that I...
View Article"Could not find scope" Failure
I have a method config that failed, giving only the message "Could not find scope correlate_genomic_event_clinical"...
View ArticleIs FireCloud down?
I can't sign in ("Error loading user information. Please try again later.") and API calls are returning 500s.
View Article>10% update_entity calls fail with 500/502 errors
When I delete large temporary files (BAMs/FASTQs/etc) from a workspace I delete the corresponding attributes using update_entity calls (https://api.firecloud.org/#!/Entities/update_entity). I...
View Articlecall caching criteria
I launched a submission without first filling in the output fields in the task config. After I filled them in, I relaunched the submission, hoping for a cache hit, but was disappointed. I would think...
View ArticleIs the observed behavior of write_lines correct?
I have a WDL task that ran in FC today. The task has some inputs. Two of them are described here. One "pcovs" comes from the user/WDL and is an array of files. The other derived from the first via...
View Articlesize arithmetic issue?
I tried to do "size arithmetic" in WDL for disk size calculation. The main objective of the size arithmetic is to calculate size of VM disk "manually" using WDL like this: call some_task { input: a=a,...
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Firecloud can't decide if a workflow is running or not..
I get one view in the "monitor" tab : and another when I chose a particular "running" workflow: Is this a bug? can I do something about it?
View ArticleCannot add simple method to namespace of which I am owner
See attached image, with all details. WDL also available at http://gdac.broadinstitute.org/runs/tmp/echo.wdl) FWIW, wdltool does not indicate anything is wrong with the WDL. My local WDLtool version is...
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