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Issue with Reference-Disk-Image #7486

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jbakerpmc opened this issue Aug 6, 2024 · 1 comment
Open

Issue with Reference-Disk-Image #7486

jbakerpmc opened this issue Aug 6, 2024 · 1 comment

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@jbakerpmc
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jbakerpmc commented Aug 6, 2024

I believe there is an error in the information provided by the Reference Disk Support in the documents for using reference disk images in gcpbatch. I believe there is a "[" missing or this bit is additional as there are 3 "[" present in the example. When trying to run this on my cromwell config, I get a syntax error. This is regarding using GCPBatch and not PAPI V2 as mentioned in some examples:

This is what I think it should look like:

reference-disk-localization-manifests = [ 
        {
            "imageIdentifier": "projects/pmc-bdc-private-test-cromwell/global/images/omics-reference-disk-image",
            "diskSizeGb": 10, 
            "files": [ 
                {
                    "path": "pmc-bdc-test-cromwell-references/hg38/v0/Homo_sapiens_assembly38.dict",
                    "crc32c": 2158779318
                },
                {
                    "path": "pmc-bdc-test-cromwell-references/hg38/v0/Homo_sapiens_assembly38.fasta",
                    "crc32c": 420322484
                },
                {
                    "path": "pmc-bdc-test-cromwell-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
                    "crc32c": 1970999569
                }
            ]
        }
    ] 

Not sure if reference-disk-localization = [] is also correct

@aednichols
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We will gladly accept a doc PR for this, docs are one of the more popular updates by the community.

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