optional inputs status
Hi Firecloud team, do the optional inputs work again? I don't want to incur a charge to test this. Thanks! -Dimitri
View ArticleAllow optional outputs (firehose parity)
Hi Firecloud team My tool in firecloud can output different kinds of files based on input flags (for example, a matlab compatible file, a pkl, a maf etc) I would like to specify output files as...
View ArticleIssue with Exporting Method to Workspace - Destination Workspace Dropdown Not...
Using Chrome 56.0.2924.87 on OS X 10.11.6. In the Method Repository when I attempt to export the method to my workspace, I can see my workspace in the dropdown "Destination Workspace:", however, I...
View ArticleIs there a more elegant way to use ${sep= } in a firecloud wdl?
Hi Firecloud team, I want to write a wdl that passes N copies of the "-b" parameter for my task. desired output: python script.py ABC -b file1.bam -b file2.bam right now I have python script.py ABC -b...
View ArticleETA on restoring 'delete' operations in API?
Could you please provide an estimate for when 'delete' operations will be re-enabled in the API? Thanks!
View ArticleRunning Indel Realigner in firecloud
Hi Firecloud team. I have a multisample individual and for consistency I want to coclean the bams together. I added samples/pairs to my individual entity, and that works well, but I need to output one...
View Articleis fuse enabled in firecloud?
I can't seem to find the answer to this on google genomics is the docker container run with: --cap-add SYS_ADMIN --device /dev/fuse ? I want to use fuse mount but I suspect it's impossible -Dimitri
View ArticleMore intelligent preemption process?
Can the preemption signal be passed along to the running docker instance? or is this a limit of google genomics? It would be cost effective to checkpoint and continue running when cromwell relaunches...
View Articlemonitor search text "sticks" across workspaces? removing text brought back...
I went into a workspace and to the submission tab and I type in a filter. I use a string of the wdl's name to find submissions only of that WDL. I later logged off of FC and then into it again and went...
View ArticleMethod Namespaces: docs do not make clear that namespaces are implicitly created
Today I tried to help a new user create a new namespace in the method repository. But after searching the docs and forum several times, I could not locate a snippet of documentation that addresses this...
View ArticleMethod Namespaces: implicit creation can be harmful, request new API methods...
In another thread I posted that today we learned that method repo namespaces seem to be implicitly created...
View Articleworkflow access inheritance
Within workspaces and workflows that are undergoing active group development (eg. rebc-oct16/rebc_template) the implementation of access rules for updated workflows do not consider inheritance from the...
View Articlenon-specific exception message?
I try to edit a method config and I see this box (see attached PNG) with a blank exception message. I think the issue is that I am "READER" on the workspace and so am unable to edit the config. {...
View ArticleUnable to Clone a workspace containing a method config
I create an empty protected access workspace - and successfully tested cloning that workspace. I populated that workspaces's data model with TSV files - and successfully tested cloning that workspace....
View ArticleError when aborting workflow
I launched a single-task workflow, which ran with operations id: EIGzm7-SKxjd85qrosWuiVEg8J7JsoIWKg9wcm9kdWN0aW9uUXVldWU The algorithm takes a long time to run (we need to fix that). I saw it was still...
View ArticleSelect multiple entities when launching analysis
This is a request for a new feature: It would be nice, if, when launching a method configuration, I could select more than on entity to launch it against. While one can create a set that contains the...
View ArticleJobs not submitting
Hi Firecloud Team, I tried to run a 4 workflow submission for a short task, and it's been an hour and none of the jobs have produced jes logs or made any indication of progress. exec.sh files have been...
View ArticleOutputs of successful jobs not stored in attributes
It looks like the outputs of successful jobs aren't always written to their corresponding attributes. For example, please take a look at these submissions (the other jobs in a set of 970 ran fine):...
View Articleno pairs leads to hanging-launch spinner for method-config of...
I have a workspace with no pairs in the data entity model. I have a method config of root-entity-type "pair" and I hit the launch button. I see a hanging spinner. If I don't hit escape it then the...
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