GATK Best practices versions
Hello dear GATK team, I was wondering about the tool versions in the GATK WDL best practices, specifically should the versions (that is the docker image) from the options json file be used or is it...
View ArticleReference - Homo_sapiens_assembly38 resource bundle
I am looking for location of equivalents for below files, out of Homo_sapiens_assembly38 resource bundle gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict...
View ArticleInsufficient permissions to set lifecycle rule
I was hoping to add a lifecycle rule (automatic deletion of files after n days) to a Google Bucket linked to our FireCloud Workspace (navigate to the bucket =>Bucket Lock => Add lifecycle rule)....
View ArticleTrouble making methods private
Hi, I'm having trouble making my methods private. When I uncheck the Publicly Readable? box for my method and save the changes the methods is still present in public tab. Is this a bug, or am I...
View ArticleFree credits expired - how to access associated bucket to copy data
Hi, I have a workspace that was created with a free credit billing account. The free credits have expired and I can no longer access the data in the bucket-is there a way I can change the billing...
View ArticleTask that takes one entity as input and outputs multiple entities (e.g....
We (and many other people) batch together multiple samples for sequencing. The resulting output file from the sequencer thus contains reads from multiple samples that then need to be split into...
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Workflow Timing: Error loading charts.
Hi there, I'm running the GATK4.1.0.0 gCNV cohort mode workflow and I get the following error for the Workflow Timing diagram: Error loading charts. Any clue why I am getting this error and how I can...
View ArticleBaseRecalibratorSpark double copying of reference input files
Hi, I am testing BaseRecalibratorSpark on GCP through wdl-runner (i.e. "gcloud alpha genomics pipelines run"), since I would like to include the Spark version of this tool in my future wdl scripts,...
View ArticlePreemptible tasks that take more than 24 hours should not restart on a...
We have encountered cases where a preemptible task takes longer than 24 hours and is therefore killed. However it is restarted again on a preemptible instance where it is killed. This process is...
View ArticleAvailability of TCGA hg38 controlled data (specifically, BAM files)
FireCloud doesn't have TCGA hg38 BAM files, is this correct? If so, how can I access them from FC? (It also seems like GDC data are not on GCP...) Thanks!
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CGA WES pipeline ICE intervals
Hi! I'm trying to use the CGA WES pipeline. I cloned the workspace broad-fc-getzlab-workflows/CGA_WES_Characterization_TCGAControlledAccess And imported my data and set up the method config for my...
View Articleupload and storage of WGS data in Firecloud
Hello, I plan to upload a large set (~100) of WGS .bam/.bai files to Firecloud. I was wondering what is the cost of uploading and storage of data (per Gb) in the Firecloud workspace? Could you please...
View ArticleMoved: VCF generation for somatic SNVs without "Normal Sample"
This discussion has been moved.
View ArticleMaking the CCLE workspace public
Dear Firecloud team, We would like to make the CCLE phase 2 workspace ( https://portal.firecloud.org/#workspaces/broad-firecloud-ccle/CCLE_v2_data) public. The data linked to in this workspace resides...
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Transient error issues
Hello, In the last week I have been running many workflows (sample sets of 1000), and each time I run into the following set of transient errors: 1) All tasks "succeed" but the workflow fails...
View ArticleCan't see jobs I've run in Monitor tab
Hello, I recently ran a task, the direct link to which is here:...
View ArticleSetting (extra) workflow options
Hi! It's not clear to me what kind of Cromwell workflow options are available in FC and how/where to add JSON. I'm specifically interested in: 1) (Global) Runtime Attributes Can I set global attribute...
View ArticleuBam ordering confusion & BGISEQ-500 platform
Hi FireCloud team! First off, thanks a lot for this great platform and tools! According to the tutorial here (https://tinyurl.com/y49aecfy), during uBam generation I should not touch the SORT_ORDER...
View ArticleVCF from Germline SNPs + INDELs Best Practice Workflow
Dear Firecloud team, I just wanted to check with you couple of things regarding the Germline SNPs + INDELs production WDL/workflow. If I am planning to run this workflow with single samples only with...
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