RFE: Help Button in web UI should link to relevant documentation
Back in the days of Firehose, clicking the help button took you to a wiki page relevant to the open page. It would be fantastic if FireCloud did the same thing. E.g. if in the data tab or clicking the...
View ArticleHow to remove unwanted entity (e.g. sample) from my workspaces?
I just want to remove some samples in my workspaces. Thanks!
View ArticleWhat is MutectFC for?
Hi, I went over the WDL of 'WXS_hg19_MutationCalling_MuTect_v1-5_BETA' task and noticed that there was a submission called 'MutectFC'. The input interval is 'MUTECT_FC_INTERVALS'...
View ArticleNeed to reset columns or clear cookies in order to see new attribute (column)...
I have a workflow that outputs an integer value. My method config maps that integer output value to a new attribute entity; e.g., nuclei_count on the sample entity. I run that method config for the...
View Articlerun mutect
Can someone point me where I can find instruction/tutorial on how to run mutect on firecloud?
View ArticleDuplicate Entities in Entity Sets
Hi FireCloud team, When uploading entities to an entity set, it is to get duplicate entities in the set if uploading an entity already present in the set. This can be frustrating, since it is only...
View Articlecan't import new method config and can't delete old one
Hi, I've deleted an old snapshot for a method configuration in the method repo and added a new snapshot for it. Now, when I go back to my workspace, I can't seem to import the new snapshot, and I'm...
View Articlehow to launch method on all samples in the workspace?
When I go to launch a method on a workspace, the GUI allows me to select which samples to run it on, but the list of available entries shown is a small subset of the total available in my workspace. Is...
View Articlemethod/workflow attributes and default configurations
Some of my workflows are leveraging the 'workspace.attribute' values and these values point to required resources for that method (ex. indexed genomes or other resource data). Instead of needing to set...
View Articlehow to ssh to a running FireCloud job node?
Is it possible to ssh into a node that's running a workflow? I've got ~500 jobs running and most are taking a lot longer than I expected. I'd like to check on a few of them to see where they're at in...
View ArticleCannot read a TSV that's bigger than 128K bytes, but I can write it!
I'm trying to create a join call-set and I have a large TSV I need to read for processing. I'm getting the following error: >message: Workflow has invalid declarations: Could not evaluate workflow...
View Article[Failed] How to fix it?
Hi, I got a FAILD message. How can I fix the issue? Restart? Thanks! WGS_hg19_MutationCalling_MuTect_v1-5 message: Unable to complete JES Api Request causedBy: message: insufficient data written Best,...
View ArticleWorkspace renaming
There should be support for renaming workspaces. We wanted to rename our workspace to _old. What we wound up doing is cloning the workspace into _old and then deleting the original. While this seems to...
View Articlefailure when running on large pair set
I launched a job on a sample set that aggregates a file on each sample to one big file on the sample set. The sample set has about 10,000 samples, and this resulted in the docker run command line being...
View Articlemessage: insufficient data written
Hi, I got the following message. One of the task is Failed. But, some other tasks are still running. It is not the first time. How can I stop them and fix it? Thanks. message: Unable to complete JES...
View Articletiming inconsistencies
I have a WDL task that's the last in a scatter (of width 10) that ran on FC. The GUI shows the information copied/pasted here: Call #10:...
View ArticleReturn code producing a failure in submission
Hi - Is there a way to tell Cromwell in FireCloud to not freak out and tell me my submission failed from a return code not equal to zero? I am going to define a run time attribute that allows me to...
View Article[PoN] What kind of data is in the PoN named "final_summed_tokens.hist.bin"
Hi, Could you please to let me know more details about the PoN named "final_summed_tokens.hist.bin". e.g. How many WGS/WES samples? How many CNA/mutatoin samples? Thanks a lot! Best, Chunyang
View ArticleIs it possible to specify workspace attribute as array of arrays?
I want to pass two-dimensional array to wdl script. Is it possible to specify it as workspace attribute or as field of entity? Thank you.
View ArticleRecent jobs stuck in "aborting" stage
Hello, I have three analyses I performed between the hours of 9:34-9:58 in the workspace nci-mjan-bi-org/SCB0024 in which all but at least one pair analysis within the pair sets successfully aborted;...
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