UX could be improved when creating a new method
When creating a new method in Firecloud, it checks that the wdl parses on injest (which is great!) however if I then try to fix the problematic file and re-import, it doesn't notice that the file has...
View ArticleFireCloud should validate methods on edit
If I edit (not create new) a method in firecloud, and it has an error (parsing), that error should be detected when I try to edit the method (as with creating a new method). but what actually happens...
View ArticleBug in "remove workspace attribute" UI
if I have several workspace attributes (entered in non-alphabetic order) and I try to remove one of them, the system actually removed one that I didn't click on. I think that it has something to do...
View ArticleFirecloud should be less "agressive" abount missing output fields in a method...
When a workflow has outputs they should up as fields in FireCloud, but sometimes as a configuration author I would like to ignore some of these outputs. While this is legal, there's a "scary" red error...
View Articleworkflow function "sub" is too impatient. Needs to wait until inputs are...
Here's an example workflow that I think should work: workflow testSub { call MakeString{} String no_and=sub(MakeString.out,"_and","") } task MakeString{ command{ echo hello_and_goodbye } runtime {...
View ArticleError messages should include the problematic input whenever possible (Disk...
For example: Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE' should be Disk strings should be of the format 'local-disk SIZE TYPE' or '/mount/point SIZE TYPE'....
View ArticleAnalysis tab should work on compressed vcfs and allow hg38 reference
The current analysis tab is currently almost unusable. It seems to only allow bam and vcf files, and it only has hg19 reference. The broad's main analysis pipeline is HG38, and produces compressed vcfs...
View ArticleDeleting un-needed submission directories
After a bout of developing a method in Firecloud one is left with many abandoned submission directories, many of which may contain large files. Some are needed (they are referenced by the data in the...
View ArticleUI typo in file preview
When previewing a file there seems to be something wrong with the output. above the window where the preview lives I see the following sentence: Last 1708 lines are shown. Use link below to view entire...
View ArticleConfusing file left in call-cached execution directory
In the current version of cromwell (v28+) there's a behavior that I haven't noticed before, there's a file call_caching_placeholder.txt which explains very clearly that this directory is empty because...
View ArticleHow to remove unwanted data from my workspaces?
Does portal.firecloud have this option?
View ArticleClik here to view.
Authorization exception... permission issue? or valid WDL/method name issue?
I try to upload a WDL, but I get this error message Error: Authorization exception for user esalinas@broadinstitute.org attempting to exercise permission Create on entity...
View ArticleJobs spend a long time "waiting for quota"
Dear FireCloud Team, I see my firecloud jobs will spend a long time (hours or days) in a "waiting for quota" state prior to execution. They are running fine, when they do execute, and they have been...
View Articlefeature request : public indicator in/for method repo (methods and configs)
In the FC method repo the items (WDLs and configs) are listed and are readable by every registered FC user if an OWNER of the item (WDL or config) sets the "Publicly Readable?" box. If one is an OWNER...
View ArticleUploading data to FireCloud bucket from Google Compute Engine in another...
I have been working on a VM in a google project called "PROJECT1" (for example) and I have data on that VM that I want to transfer to FireCloud. My FireCloud workspace is under a different google...
View ArticleIncorrect error message when task fails to complete
When a task returned with an error code, and also one or more of the output files is missing, the "failure" that is reported is that the file couldn't be transferred. While this is technically true,...
View ArticleMonitor claims "Call caching: Disabled" erroneously
In the first few seconds of a submission (before it actually gets going) the Monitor will state that a certain submission has Call Caching disabled even though this isn't true. A frantic refresh will...
View ArticleCan there be a rational order to the call in the monitor view?
...or perhaps there is one, but it's beyond me. Here are the calls I see (together, for your enjoyment, the order in which they show up in the timing diagram): {{ 3. CheckBuild 2. dbRsIDsSize_string 6....
View ArticleCan the order of the inputs and outputs to a method config be displayed in a...
This is a similar request to a previous one of mine, but it's different. In a method config the order of the inputs (and outputs) is seemingly arbitrary: QCAndPrePhase.dataset_fam: (File)this.fam...
View ArticleFeature request: ability to add notes (free text) to a submission
For use in production one often needs to annotate submissions ("use this", "this failed because....", "need to look," etc.) it would be nice if there was the ability to annotate submissions (140...
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