System just logged me out during a session
Working in Workspace when system logged me out. Also change the day/time for Linking my NIH account.
View ArticleWhen will the FireCloud access be available outside of Broad?
When will the FireCloud access be available outside of Broad? I am waiting for my account to be activated. Thanks! Christopher Christopher Dubay, PhD Biomedical Informatics Program Manager Laboratory...
View ArticleUI/bucket job status inconsistencies?
In the UI, a submission seems to be in an error state. The attached PDF from the UI shows that one of 5 tasks (conttest) is still running and that there is a red "Done!" status button. In seeming...
View Articlecan't launch a method on a pair if another pair has arrays in a field? or...
I launched a WDL/method "esalinas/CallingGroupSnapshot ID: 8" on one of two pairs in my workspace. An attached PNG shows that pair #1 of two pairs has fields in the data model filled out from the...
View ArticleMethod repo filtering doesn't include namespace
A common way I would want to filter the methods I see in the workspace repository is to only look at methods from a particular namespace -- for example, all of the GDAC methods have the same namespace....
View ArticleInternal server error viewing the monitor for a task
I submitted a job to the workspace broad-firecloud-testing/API_TEST but clicking on the monitor gives an internal server error Workflow ID: 30c3e8c8-482e-47c6-bec1-82d00c974490 Submission ID:...
View ArticleJob fails silently when the Docker image+tag doesn't exist
I submitted a job that failed without any standard error or standard output, with no explanation. In order to see what went wrong, I had to go into the developer console and look at the JES log, which...
View Articlesubmission timeouts related to number of tasks/jobs in WDL?
I made a "toy" workflow that seems to run fine. It calls a single task. It's a "tiny" hello world. I redid it in "mega" style where the task is called 1000 times. During attempted submission of the...
View ArticleAvailable pipleines and tools on firecloud
Hi, Is there a list of tools and pipelines available on firecloud somewhere? I am specifically interested to know if GATK toolkit and all of the Broad's Cancer Genome Analysis group (CGA) modules like...
View ArticleSSL Error pushing WDLs
This issue has already been resolved, but in case anyone else has the same issue, I wanted to post it to the forum. When trying to push a WDL to the method repository from my local machine, I get the...
View Articleconvenience button for setting outputs in a method configuration
When defining the method config's outputs, I type into each box an expression ("this.Report" for example). This is a data-entry process. Could there be a convenience button (perhaps called something...
View Articlecommented WDL line but not?
I have a line in my WDL command that looks like this "#source /usr/local/run_OrientationBias_filter.sh ${ID} ${BAM} ${MAF} ${REFERENCE} ${DBSNP} ${CONTEXT} ${ALTALLELE} ${STUB} ${OUT} ;" See that the...
View Articlemove add_new button for WS attributes ABOVE the fields? instead of below?
currently the "Add New +" button for adding workspace attributes is below a list of existing attributes (see attached figure/screenshot crop) Because of the buttons layout position, any "rapid-fire"...
View Articleworkspace attribute key/value text fields bigger? or somehow show filenames...
can we make the fields, particularly for the values (of the key/value pair) bigger? the values often contain GS URLs which are big. see attached The beginning of the URL (the first characters of the...
View Articletimeout needs notice
I have lost count of the number of times that I have been updating attributes on the workspace or editing items in the method config and the firecloud logs me and and my work is unsaved. If firecloud...
View Articlepassing a DIRECTORY to firecloud?
Is it possible to pass a directory via a method config to a WDL? From what I understand to pass a directory, I'd have to zip it up, is that right? Even if I do zip a file, a LOT of disk space could...
View Articlecannot delete a method configuration if its source WDL is deleted
I deleted(aka REDACT) a method in the method repo but when I tried to delete a method config that had used it in a workspace I got an error "Cannot get esalinas/lars.ready/1 from method repo." Should I...
View Articlemore helpful error message during method config submission?
I try to submit a method config with a root-entity type of "sample set" but got the error below.... Can FC have a better error reporting? I was able to submit because I noted that I had mispelled a...
View Articleerror during method conf launch, my browser stays in config screen, but...
I tried to submit a method config but got an error (as shown here http://gatkforums.broadinstitute.org/firecloud/discussion/7361/more-helpful-error-message-during-method-config-submission ) Given two...
View Articleunable to delete a method config but the WDL in the repo is still there
Error 500: Cannot delete or update a parent row: a foreign key constraint fails (`rawls`.`SUBMISSION`, CONSTRAINT `FK_SUB_METHOD_CONFIG` FOREIGN KEY (`METHOD_CONFIG_ID`) REFERENCES `METHOD_CONFIG`...
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