use of a target bed in Broad_MutationCalling_Mutect_Workflow
Hi If I want to restrict variant calling over my own target BED, which workspace attributes can I use to point to my target BED? What is the difference between AGILENT_INTERVALS and...
View ArticleWorkflow which takes ~11 mins on laptop took ~11 hours on FireCloud
We think this is an apples to apples comparison. I've attached the workflow log from both local and Firecloud execution, as well as the WDL (which has 4 tasks). The firecloud workflow execution ID was...
View Articlepre-populated TCGA workspaces
Hi I have access to TCGA controlled datasets, and I was able to link my FireCloud account to my eRA Commons. I can see the list of controlled TCGA datasets available in the data library, however, I do...
View ArticleFeature Request: Filter sample in data tab by sample_set
When looking at the data tab of a workspace I sometimes have multiple sample_sets. It would be very helpful to be able to filter the list of samples by sample_set so I can look at results from only one...
View ArticleFeature Request: Workspace History
Hi FireCloud team, Would it be possible to have a simple "workspace history" feature? This may be worthwhile for audits of workspaces, when users are picking up a project after some time, and seeing if...
View ArticleWorkspaces cloned from Data Library are not showing up in the list of workspaces
Hi I have cloned multiple times workspaces from those listed in the data library, but once cloned they are not showing up in my list of workspaces. Is this a bug? Note that i can successfully clone...
View ArticleOccasionally jobs get "stuck"
Sometimes when running a workflow a single task will appear to have completed (there are stderr and stdout) but firecloud doesn't register the job as finished. The timing diagram will show it still...
View ArticleCromwell Polling Interval is sometimes too long
Sometimes the Cromwell Polling Interval in the timing diagram is extremely long and can be disproportionate to the amount of time the task takes. For example, in a recent workflow a task that took 2...
View ArticleFailed job with no output clue
Hi Workflow "bam_dates_workflow" in workspace broad-firecloud-pcawg/damage is failing despite that it runs fine on a google VM using cromwell and the same input parameters and files used by the...
View ArticleCan you squash a rumor about the need for Python in docker containers that...
A bit of an odd question, so please bear with me. I came across this comment # As of this writing, firecloud has an implicit requirement for a full python installation # This should become unnecessary...
View ArticleControlled access TCGA data cannot be copied into user workspace
Hi, when I was trying to import controlled access TCGA data into our own workspace, we get the following error: Error 422: Source workspace broad-firecloud-tcga/TCGA_OV_ControlledAccess_V1-0_DATA has...
View ArticleNew user cannot register
I am a new graduate student at the Broad and I am trying to register as a new FireCloud user. Upon following the registration instructions by going to firecloud.org and clicking "Use FireCloud", I am...
View ArticleFile streaming
I have broken down some of the time that is lost in running tasks in firecloud. In this example, I am running coverage collection on a single whole exome bam from the co-located tcga bucket, 12GB in...
View Articleagain : conntect timed out
Reffering to http://gatkforums.broadinstitute.org/firecloud/discussion/8805/connect-timed-out#latest I submitted the same WDL, but on a different data entity than the data entity used for the...
View ArticleWorkflow hung because incorrectly reporting scatter task as still running
We observed this in a benchmarking run of the best practice QC workflow on 1000 BRCA tumor/normal pairs. Of the 1000 workflows, 991 succeeded, 5 failed, and 4 are still flagged as running. This is an...
View ArticleWorkflow reported as running, but is stalled at its start
We observed this in a benchmarking run of the best practice QC workflow on 1000 BRCA tumor/normal pairs. Of the 1000 workflows, 991 succeeded, 5 failed, and 4 are still flagged as running. This is an...
View ArticleWorkflow is hung in one scatter task
We observed this in a benchmarking run of the best practice QC workflow on 1000 BRCA tumor/normal pairs. Of the 1000 workflows, 991 succeeded, 5 failed, and 4 are still flagged as running. This is an...
View Articlemethod repository can not be imported
Dear sirs , I am glad to congratulate you with Christmas and wish you all the best. But let's return to the work. I lost an opportunity to import any new methods in workspaces. It started from around...
View ArticleFireCloud does not return useful error information for common user error...
I am running a workflow with an input parameter that is set to a workspace attribute (CA_PON_MUTECT). I misspelled the attribute name in the workspace attribute definition section, spelling it...
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Inconsistencies with color-coding in workflow timing diagram
When viewing workflow timing diagrams for two completed workflows, the color-coding appears to be different when hovering over the same processes and steps. Both of the workflows completed and ran...
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