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BUG: method description in method configuration is not parsing markdown

I have a method in the repository whose description is formatted with markdown. When I view that description in the method repository, the description is correctly displayed (i.e., the markdown is...

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Samtofastq Method Config.

Hi, I am new to FireCloud. I was wondering if it is possible to revert BAMs to FASTQ, then merge multiple FASTQ from different runs for one sample, and then align back - all in FireCloud. I first tried...

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I am unable to launch jobs.

Clicking on launch results in the spinner for about 10 seconds and then nothing. Going to status.firecloud.or indicates the user profile service is down. See attached screen shot.

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Issues with uploading

Is there a lag time between when a service account is registered with firecloud, added to the FireCloud workspace and when the service account can beging adding files to the bucket associated with the...

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Positivo control for MUTECT2 evaluate locally

Dear, I would like a bam files (Tumor-paired), with known mutations identified by MUTECT, for me to run locally and evaluate the program if I am running correctly. Is there somewhere I can get. Because...

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How can I realign BAMs?

I got BAM files different convention of locations than the ones the used at FC. How cant i realign these files?

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Many "Lock wait timeout exceeded" errors today

Are we having Firecloud database problems today? Nearly everything I've tried to do in workspace rebc-oct16/rebc_template results in a "Lock wait timeout exceeded" error. Among the things that do not...

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Task in "Running" state a day after stderr says it failed

I have a workflow (ID 48e54c59-9d56-4dd7-8745-a5cca7ccaa30) where a task failed a day ago according to the stderr: Exception in thread Thread-3: Traceback (most recent call last): File...

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Inconsistency in naming of downloaded TSV files

If I go to a workspace and download the metadata for the participant, sample and pair entities, FireCloud generates participant.txt, sample.txt and pair.txt files. These are the TSV-formatted files...

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opendj-priv.dsde-prod.broadinstitute.org:636; socket closed

Several jobs (4 of 36) in workspace rebc-oct16/rebc_template failed in workflow consensus_1orMore_maf with message: "opendj-priv.dsde-prod.broadinstitute.org:636; socket closed" and no other clue. Do...

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BUG(?): Trouble with Data UI

Hi all! I'm experiencing some interesting phenomena with the FireCloud UI. I've been deleting entities using the API and this seems to have triggered some issue. When I initially go to the workspace...

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I set up the preemptible as 1, but the job was re-run 4 times

Dear Firecloud team, There should something wrong with the preemptible. I set the value as 1, but it rerun 4 times. Here is my workflow id: Workflow ID:2370d038-a69e-4951-b299-a89478084f89 Thanks, Hailei

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request: reduce size of new graphic on firecloud.org page

The new graphic on the firecloud.org page is so large than I need to scroll down to click on Use FireCloud, Blog, Forum etc. A minor usability issue, but a pain nevertheless. thanks, Chet

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WDL window not expanding in Chrome

Hi, I'm trying to view the WDL script in my method configuration in Firecloud, but the WDL window won't expand in Chrome. It does work in Safari. Screen shot and chrome console error attached. Do you...

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Error running WDL in workspace, insufficient permissions

Hello, I'm trying to launch analysis using a method that I own on samples in a workspace that I own and am getting this error: Error: insufficient permissions to perform operation on *name of workspace...

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Trouble getting output from a bucket; also finding buckets for TCGA bams

Despite being a developer of a tool that runs on Firecloud all the time, I have never actually used Firecloud (or Firehose), so please do not underestimate my ignorance for the following. . . We're...

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FireCloud is listed as unverified

Google has just warned me about FireCloud being an unverified developer therefore incurs a security risk for my google account. I guess broad should straighten this up with google.

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Failed to localize files error

I am trying to run amaro/pick_absolute_solution in the Wu_DCIS_WES_analysis workspace but keep getting variants of "Failed to localize files", see below for an example: Please see...

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Can't add user?

Hi Y'all, We have a Firecloud project set up: https://portal.firecloud.org/#billing/firecloud-cgl And I've added a few users already with no problems. We all have @ucsc.edu email addresses, which are...

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joint discovery error in 3 samples of WGS

When I ran this execution in fire cloud. I got the error message. message: Task JointGenotyping.ImportGVCFs:23:1 failed. JES error code 5. Message: 10: Failed to delocalize files: failed to copy the...

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