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message: Unexpected failure in EJEA. (again)

Hi Firecloud team, I saw that a few weeks ago there was a post about a similar error. I tried to run a test workflow that previously worked yesterday, and got this error. message: Unexpected failure in...

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Cannot log into forum

Hi Firecloud team, I tried to log in with my google account, but got 400 error:redirect_uri_mismatch I had to create this temporary account to report this. I tried on two computers and had the same...

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Cannot find or see tutorial or shared workspaces in firecloud

Hello, Since I have gained access to FireCloud, I have been unable to see any workspaces on FireCloud, including the tutorial workflows. In what I think may be a related issue, I am also unable to...

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An array of files as an entity attribute in data model

I didn't see this in the documentation, but I might have missed it. Is it possible to specify an array of files as a data model entity attribute? I have a genetics data set, with participants and...

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Upload of partial pair metadata

I found that when uploading a pair meta-data file that all association columns (participant id, case sample, control sample) are required. Are we not allowed to do partial updates of data? e.g. add a...

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What is the status of file streaming?

File copying is still an issue, and there was some discussion about allowing signed urls, or some other method of allowing random file access without copying the entire bam in. (a lot of downstream...

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Job stuck in the running state

My workflow (attached) ran and has a job stuck in the running state. The first task, bsmap ran and succeeded (the job outputs are in the appropriate google buckets) and status is properly...

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RFE: RESTful api needs a workspace rename feature

I am currently not seeing such at https://api.firecloud.org/#/Workspaces Thank you, Mike

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Cryptic error message in Firecloud job execution

Hello, I am running the method configuration "ebert-pipeline2" from my workspace "ebert-pipeline-test". When I begin running the pipeline on a sample, Firecloud can copy the files correctly and begin...

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Cannot access hg38 open access workspaces in FireCloud Data Library

We created open and controlled access workspaces for each of the hg38-harmonized TCGA cohorts (cancer types). The controlled access workspaces are in the TCGA-dbGaP-authorized authorization domain, the...

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Need info on how to create a sample_set in the FireCloud Basics section

I was a bit lost in the Methods Configuration section, specifically under the "Workflow Expansion Expressions" subsection. I want to be able to run my workflow on each of the samples in a sample_set,...

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July 19th release has broken GDC file retrieval

We run workflows to download files from the GDC and copy them into cloud storage. The two workflows are: broadinstitute_cga/gdc_file_downloader/1 broadinstitute_cga/gdc_bam_downloader/1 The workflows...

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Error recreating a previously deleted method

In Method Repository, I created a method GenomeStrip/RunScript, but then at some point I accidentally redacted it. However, when I try to create another incarnation of GenomeStrip/RunScript, I get the...

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Mismatched statuses getting worse

Hi Firecloud team, I've encountered this bug across two different billing projects over the last two days, every time I run a job with ~200 submissions. When in the monitor tab, When I look at the...

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Data model not updated

Hi Firecloud team, Is this a regression, a bug, or not intended functionality: I am trying to run a workflow, but I don't want to write all outputs to annotations because it clutters the workspace....

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Running jobs not terminated when workflow is aborted, incurring cost

Hi Firecloud Team, I terminated a submission in Firecloud (~100 workflows, 88 were running) The workflow is marked as "Aborted" in Firecloud, but the VMs were not terminated (88 are still marked as...

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Workspace clones & inheriting permissions

Hi, As best I can tell, workspace clones don't appear to inherit permissions (in my case, read permissions) from the original parent workspace. Is this correct? If so, is this intentional? It seems...

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Any way to download hellbender-all-1.0.jar?

Hi, I'm trying to reproduce some Firecloud best practice workflows locally. However, some files used in the workflows could not be downloaded. For example, /usr/local/bin/hellbender-all-1.0.jar was...

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More retries than preemptible setting?

I'm having trouble interpreting one of my timing diagrams. One of my workflows seems to have retried more times than my preemptible setting (which was 3). Granted the task...

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"Could not capture docker logs" error

Hi, I'm encountering an error I can't explain while testing a new method (MELT; see http://melt.igs.umaryland.edu/) on a single ~30X human whole-genome sample in FireCloud. The error message returned...

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