Beri
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Recent activity by Beri
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The requirements in the workflow WDL header states ## Requirements/expectations :## - Pair-end sequencing data in unmapped BAM (uBAM) format## - One or more read groups, one per uBAM file, all bel...
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Yes, you'll just need to change the workflow attribute configurations to hg38 reference data. You can find hg38 equivalent reference files for mutect2 here: https://console.cloud.google.com/storage...
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If your trying to access TCGA data files like bam or fastq then its most likely due to the Service Incident, it's in the process of being resolved. As a workaround you could download the TCGA files...
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Hi Sam, No there isn't something like that currently available but I can see how that can be valuable for Project Owners. I'll create a feature request for this and perhaps it can be added to Terra...
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What genome version are you trying to access? Might be related to this Service Incident https://support.terra.bio/hc/en-us/articles/360033213412-Service-Incident-September-9-2019-TCGA-datasets-hg19...
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Danny, Was the data downloader able to get access?
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Hi Danny, That should cover all the steps to obtaining access to TCGA workspaces. It may take some time for the permissions from dbgap to be transferred over to Terra, max 3 days. How long has it b...
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Hi Beth, I spoke with the dev team and they mentioned most of these are already installed and current pkgs = c("Rsamtools", "data.table", "qqman", "RColorBrewer", "tidyr", "dplyr")pkgs %in% rownam...
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Hi Beth, What do you mean by "Bioconductor preconfigured notebooks"?
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You can download a json file listing all the submissions of a workspace using the Terra/Firecloud swager api page : https://api.firecloud.org/#!/Submissions/listSubmissions The low tech option woul...
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