Configuring Array of Strings with One Element
I have an array of strings that will often just have one string as an input. How should this be formatted when configuring? In the exec.sh it seems that when just a string is entered, the parsing...
View ArticleVariable that refers to workspace bucket
It would be nice to be able to enter: "${BUCKET}/my_file.xt" instead of having to copy and bucket the bucket id: "gs://fc-fb46edeb-f05e-45c9-88f7-9ef83d8f1aac/my_file.txt"
View Article[ERROR] com.google.cloud.storage.StorageException
Hi, I got the following ERROR when I ran GATK4 Mutect2 pipeline. Is it a NIO related issue? Or, Can I fix it by turning off NIO mode? Thanks! 06:33:45.601 INFO ProgressMeter - 14:25095814 1026.0...
View ArticleNo Space Left on Device
Hello! I'm currently running WGS data on 31 samples through the default "processing-for-variant-discovery-gatk4" workflow. When ran my uBAMs through, I noticed that roughly half of them failed at the...
View ArticleAnalysis not Running
I am launching an analysis that took ~5 minutes to completely run through yesterday. The analysis submits properly and outputs the exec.sh file in the bucket. Then nothing happens, although it shows as...
View ArticleDo not require quoting String variables in the user interface
A common error I see among users is forgetting quote strings-it would be nice if quotes were not required when entering values in the FireCloud user interface. Thanks.
View ArticleHow to a Close Billing Account
Hi, I want to shut down one of my billing account. Can you please help me? Or, can I completely closed it by clicking "Disable billing" in GCP page so that this account will not be charged any more....
View ArticleFeature Req: support for requestor-pays buckets for gcr.io-based docker...
I have some docker images I want to store on Google Cloud Repository (gcr.io). There is no IP precluding public access, so I don't need to jump through the hoops that would otherwise be required to...
View ArticleHow do i get usage statistics of Firecloud?
I want to know how many registered users on firecloud, the type of processing they are doing, the total execution time of all the queries by the users.
View ArticlePoN creation error
I'm trying to create a PoN but keep getting the following error in the merge_pons stage: message: Workflow failed causedBy: message: Call input and runtime attributes evaluation failed for merge_pons...
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Random errors
I ran a workflow of 100 jobs and 7 just didn't start. I will re-start them but this is a new issue because I used to be able to run 1000+ jobs without issue.
View ArticleSetting up an institutional account
I would like to start working in the FireCloud environment and was able to create a "personal" billing account and access the service to try it out. To establish an institutional account, I followed...
View ArticleBug: help-gatk/Somatic-SNVs-Indels-GATK4/method-configs/gatk/mutect2-gatk4
workspace.ref_fasta_index should be workspace.ref_fai extra space in this. bamout_index
View Articlescopes required for https://api.firecloud.org/api/workspaces
Hi Firecloud Team, I run a small webapp built on top of the firecloud api for my group. As of very recently started getting: ``Bearer error="insufficient_scope", error_description="Different scope(s)...
View ArticleNovice to FireCloud & BioInformatics
Hi Guys, Im new to the world of sequencing and have started using the Oxford nanopore Tech MinION in my lab. I have managed to do RNAseq and WGS using it and got as far as using terminal to get Bam/Sam...
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Error 400 : Logging into FireCloud with my Google Account
I am getting the attached error on logging into FireCloud with my Google Account. I saw a previous post from someone with the same error (July 2017) that said they thought this was fixed. Still...
View Articleseeking a full enumeration of workflow submission states
What is the set of possible states returned by the listSubmissions API ? To date we've observed that the workflowStatuses field can have these values 'Succeeded' 'Failed' 'Running' 'NotRun' but surmise...
View ArticleRawls failure in 10 of 402 workflows launched in single submission.
I launched a complex workflow (a version of CGA's production analysis workflow) on 402 sample pairs. 392 of the workflows successfully launched and completed, 10 of the workflows failed to launch, with...
View ArticleIs there a simple way to regenerate the directory structure of scattered files?
It's a common paradigm for tools to expect files to be organized in a certain way. Is there a simple way to preserve the initial organization of files? E.g. They are loaded in a directory in the...
View ArticlePON used in Somatic-SNVs-Indels-GATK4 featured workspace
Hi, I was wondering if there was a description somewhere of how the PON defined in workspace attributes of the Somatic-SNVs-Indels-GATK4 featured workspace was generated. It lives in the gatk-test-data...
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