How can a method configuration locate a file generated by WDL method...
I have a task that creates a file of file paths via the WDL method ${write_lines(Array[File])}. However, upon running, it fails with the error of not being able to find the file that was generated. See...
View ArticleHow can I find the version of MuTect2 in...
Hi Jason, I see for broadinstitute_cga/MutationCalling_Mutect_v1-2_BETA_cfg (described here) that MuTect1 uses the v1.1.6 jar but MuTect2 uses /usr/local/bin/GenomeAnalysisTK.jar. Is there a way I can...
View ArticleIs there an updated MutationCalling_Mutect_v1-2_BETA_cfg?
I'm asking because the CallingGroup_Workflow within the MutationCalling_Mutect_v1-2_BETA_cfg produces a wdltool error: java -jar $wdltool graph --all MutationCalling_Mutect_v1-2_BETA_cfg.txt >...
View ArticleTask should fail if File output is not known in advance.
Hi, I had problems when using the following task: task Uniquify{ File file Int disk_size command <<< out=$(python <(echo "print(str(uuid.uuid4()))").g.vcf.gz && cp ${file} $out echo...
View ArticleFirecloud Feature request: Remove old (failed) runs together with their data
I have a workspace with lots of failed workflow runs. Each of these is associated with a submittion folder which has lots of files for which I'm paying for storage. I would like to be able to remove a...
View ArticleNamespace permissions
While testing for the feature - As a tool developer or analyst, you can update the permissions on a Method Repository namespace so you can control who can contribute to that namespace. - we found that...
View ArticleNavigating to results can be simplified in FireCloud UI
Not sure if this should be sent to the help@firecloud email (and turned into a ticket) or here. But, see attached images: my goal was to view the results of task as a Nozzle summary report. It seems at...
View ArticleDocumentation on workspace attributes
The documentation here - https://software.broadinstitute.org/firecloud/guide/topic?name=firecloud-basics#workspace-attributes is missing screenshots/pictures to be able to use and understand the...
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 Articlesignificance of out.log?
In a task that completed successfully in FireCloud, I find a file called "out.log". It seems to be a table of file data and/or transfers, perhaps a listing or manifest file. However, the file seems...
View Article64 core vm problem
We tried launching a job using a 64 core VM, which we were under the impression were now supported. However, the job seems to be stuck, and has not yet emitted a JES log after a couple hours. Gordon...
View Articlepayment for use of uploaded tools
Hey Firecloud Given the difficulty of uploading tools / debugging wdl problems etc. Can you implement a system for payment to the task creator upon tool use? Even 10 cents or something per use would...
View ArticleBilling Management
When there are two projects listed under billing management, how do you assign the cost of running a workflow to one of the accounts?
View Articleallowing creation of dependant entities from tsv
Hi Firecloud team, I am trying to import samples into my workspace, but before I do this I have to cut out the "participant" column, rename it to "entity:participant_id" and import that first. When I...
View ArticleMethod export fails
Trying to export a method from the repo to a workspace (see attached image for details) fails, with the following stack trace appearing at the console. Thanks, Mike compiled.js?t=1484753315303:2957...
View ArticlelistMethod api calsl should have a namespace parameter
It would be useful if the API call https://api.firecloud.org/#!/Method_Repository/listMethodRepositoryMethods https://api.firecloud.org/#!/Method_Repository/listMethodRepositoryConfigurations accepted...
View ArticleAllow on fail/optional tasks in workflows
In firehose you could specify tasks to run either "onSuccess", "onFail", or "Optional" after the previous task. (e.g. try the low memory option first, if it fails try the more expensive one.) This...
View ArticleRFE: need API and UI mechanism for deleting DONE jobs (submission results)
I suspect I'm not the first to ask for this, but presently neither the API nor the UI expose a means by which submissions in DONE state may be deleted. Like usual, we'd love to see this as an API call...
View ArticleFailed Analysis on Broad_MutationCalling_Mutect_Workflow_BestPractice_OA
Hello, First, I was able to successfully run 2 submissions within the workspace MiniMutationCalling_V1_Tutorial. One on each of the HCC pairs and they both succeeded. As a next step, I cloned the...
View Article