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How can one tell if a WDL or tool is NIO compatible? Do I look at the WDL, the tool code, or just the version of Cromwell? The question comes down to which public workspaces or methods will give the NIO reduced-file-localization advantage. Should I…
Hi, I have the same problem as Julia above. Thinking a little further, as well. Issue 1. To link a billing account to FireCloud, it must be newly created inside FireCloud. I have tried using my existing GCP billing account and the interface just h…
Further to Convert Fastqs to Unmapped BAM on GCP above, I was able to use the https://github.com/gatk-workflows/seq-format-conversion to create the .unmapped.bam files for the large datasets - 48 normal .fq.gz and 64 tumor .fq.gz in only 2 hours. I …
I should mention that what I referred to as .fastq files above are .fq.gz files.
Convert Fastqs to Unmapped BAM on GCP Further to the above, I see that the Broadies are ahead of me, as expected. I have located the paired-fastq-to-unmapped-bam.wdl script at https://github.com/gatk-workflows/seq-format-conversion. Thank you. Unl…
I am running the GATK Best Practices pipeline on Google Cloud Platform (GCP). I have run the tutorials with some success. My 1.4TB of tumor/normal .fastq files were delivered to me in a GCP bucket. For a further test and to meet the uBAM requiremen…
Hi BITeam, I have read through and like the idea of the free cloud portal (Thanks!). Right now I don't have a project to charge GCP time, so need to use my Mac (i7/4core, plenty of RAM/SSD) for some .org cancer work. I see the HaplotypeCallerSpark b…