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...)
TCGA open access data is available to all FireCloud users through FC but to access workspaces in FireCloud containing controlled access data, you must have an eRA Commons or NIH account with dbGaP authorization; and link your FireCloud account to that eRA Commons or NIH account.
Are you asking about access to an actual TCGA hg38 bam file resource - a test file?
I have an access to the controlled data containing workspaces through eRA Commons.
I checked this article (https://gatkforums.broadinstitute.org/firecloud/discussion/10382/populating-hg38-tcga-and-target-workspaces-with-data-files) and wonder whether there is any update in last 1.5yr.
Controlled data on hg19 build have BAM, MAF, TXT, but for hg38 build, BAM doesn't seem to be available (only BCR XML, MAF, TSV, TXT, VCF). Also there is no method configuration for hg38 BAM import from GDC.
I want to know whether there is any way to use GDC hg38 BAM files without downloading/uploading.
@SChaluvadi: @abaumann can update you for the timeline regarding the availability of hg38 data on firecloud. Recently he told me that the GDC has placed the files on the Google Cloud, and by the end of the month the hg38 tcga workspaces will be updated to reference these files. I don't know whether that will be by explicitly writing the files' gs URLs into the workspace attributes, or behind the scenes support for uuid-to-url resolution.
So I can access TCGA hg38 BAM files using gs URLs "now"? How's the authentication work between GDC/GCP/FC?
The files are on a google bucket I believe, but I don't know where. Either workspaces need to be created to reference those files explicitly, through gs URLs, or the current workspaces, which reference the files via GDC UUIDs, could be used PROVIDED uuid-to-url resolution is operational in firecloud. I don't know the details. Members of the the FireCloud support team will need to provide you with the answers.
@aboynton I'll check on this for you and let you know!
@shbrief You can't access those files with the gs:// URLs but work to get those TCGA hg38 workspaces is underway and we are hoping to have them set up by mid-march. I can keep you posted on this thread when that work is completed.
Thanks! And yes, it'll be great to get the update.
@shbrief No problem - I have it noted and will let you know when I get word that those workspaces are ready to go!