Problem with display of workspaces and faceted search
(It is unclear whether these issues appeared with the latest Sept 7 release or preceded that release.) I log into FireCloud with a google account that has been linked to an eRA commons account. Under...
View ArticleRegression in API endpoint: GET /api/methods
The get single method API endpoint (GET https://api.firecloud.org/api/methods) has a query parameter called onlyPayload that is supposed to toggle the behavior of only returning the WDL payload for the...
View ArticleFailure in firecloud despite success locally
Hi-- I have a method that succeeds locally yet fails when run in FireCloud (discussed this with @Ruchi at Fc office hours). I wrote the docker file being used in this method (image available here:...
View ArticleRemoving workflows stuck in the 'submitted' or 'aborting' state
We have 6 workflow submissions in the "broad-firecloud-methylation/Methylation_Pipeline" workspace that have failed but are still listed with either a "Submitted" or "Aborted" status on the Monitor...
View ArticleHow to build a Mutect Filtering PoN
Hi, Does anyone have a sense of Mutect Filtering PoN, like "final_summed_tokens.hist.bin". I want to try to build one. But, I don't know how. Thank you very much! I will really appreciate your help....
View ArticleBug in preview of meta-data import file
When I choose a file to import into the metadata there's a preview of the file. It used to work well, but now it fails to split the lines, putting the entire content of the file in one line. This makes...
View ArticleGive a user group permissions to a workspace
I would like to give a user group (aryeelab) permission to a specific workspace (broad-firecloud-methylation/Methylation_Pipeline). Where should I direct a request like this? In this case, I'm not sure...
View ArticleBug: method redaction checkbox doesn't seem to be working
I can redact a method by clicking on it directly in the methods repo and then clicking "Redact". No problem. But I recently made a new version (#7) of my method by editing the old one (#6) and I...
View ArticleTasks that should be call-caching aren't
I'm running a workflow that I just aborted halfway through and then restarted, expecting that all of the completed tasks from the original run would call-cache. While most of them did... some did not....
View ArticleWeirdness: workflow seems to have reset in the middle of a run
Hi guys, Something weird happened in my workflow that I've been asked to report to you under the umbrella of "making the product better" (I don't really care personally, but other users likely will)....
View ArticleJES error code 10
I saw the following error on a scatter job: message: Task fastqtl_workflow.fastqtl_permutations_scatter:194:1 failed. JES error code 10. Message: 15: Gsutil failed: Could not capture docker logs:...
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How to understand Google Cloud Project in the context of FireCloud?
Project is a central concept in the setting of Google Cloud platform. Could someone explain what roles does it play in FireCloud? How are Google projects tracked to Google billing in FireCloud? Thanks.
View ArticleCurl command to retrieve firecloud usage statistics is failing.
I generate weekly FireCloud Usage Metrics report for the NCI from usage data I retrieve from FireCloud. Each week I run the curl command: curl -X GET --header "Accept: application/json" -H...
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Unable to share workspace
Hello, I am trying to share a workspace with my lab members. However, when they accept the invite they keep getting an error message saying "This workspace does not exist". I can definitely see the...
View Article[ERROR] token_pon_size_update
Hi, I ran “token_pon_size_update” two times to build a PoN using hundreds of TCGA blood samples. But, each of them finally failed because of a file transfer issue. Should I try to run the tasks...
View ArticleBug: Cromwell removes empty spaces from WDL when creating exec.sh
This doesn't sound like a bug, but it means that the following task is edited prior to submission: workflow hello { call HelloWorld{} } task HelloWorld { command{ echo "hello and goodbye." cat...
View ArticleJobs marked as 'Running' but not executing
For example: Submission ID: 7973aa29-1d26-4868-aa68-8e20ba50956e Workflow ID: 5827b887-fbf1-4029-89dd-1013ef008e71
View ArticleFireCloud jobs fail with no stdout, stderr, and minimal JES log
I'm seeing behavior similar to two previous posts: https://gatkforums.broadinstitute.org/firecloud/discussion/10262/failure-to-delocalize-files-when-using-my-own-docker-image...
View Article"recapseg_bed" should be "recapseg_tsv" in "gatk_cov_pull" ?
Hi, For "gatk_cov_pull" in Firecloud, the input file "recapseg_bed" should be a GATK-style tsv file based on manual of "CalculateTargetCoverage". So, "recapseg_bed" is a little bit misleading. Is that...
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