Reference store sequences as reference

[dgoswamia]

how to use the reference store sequences as reference, as I followed the few workshops, and in these instructions were shown on how to create a reference store and store reference human seq and so on but I have not seen a way how this reference store stored references in the parameter-input.json

For example, in the GATK workflow workshop, the workflow was run fastq sequences were used that was registered as ReadSet for using the following parameter-input.json with s3 stored reference,

``
{
"sample_name": "NA12878_20K",
"fastq_1": "omics://account-id.storage.region.amazonaws.com/sequence-store-id/readSet/read-set-id/source1",
"fastq_2": "omics://account-id.storage.region.amazonaws.com/sequence-store-id/readSet/read-set-id/source2",
"readgroup_name": "NA12878",
"library_name": "Solexa-NA12878",
"platform_name": "Illumina",
"run_date": "2016-09-01T02:00:00+0200",
"sequencing_center": "ABCD",
"ref_fasta": "s3://aws-genomics-static-<AWS_REGION>/omics-workshop/data/references/hg38/Homo_sapiens_assembly38.fasta",
"dbSNP_vcf": "s3://aws-genomics-static-<AWS_REGION>/omics-workshop/data/references/hg38/Homo_sapiens_assembly38.dbsnp138.vcf",
"Mills_1000G_indels_vcf": "s3://aws-genomics-static-<AWS_REGION>/omics-workshop/data/references/hg38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"known_indels_vcf": "s3://aws-genomics-static-<AWS_REGION>/omics-workshop/data/references/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz",
"scattered_calling_intervals_archive": "s3://aws-genomics-static-<AWS_REGION>/omics-workshop/intervals.tar.gz",
"gatk_docker": "AWS_ACCOUNT_ID.dkr.ecr.<AWS_REGION>.amazonaws.com/gatk:4.1.9.0",
"gotc_docker": "AWS_ACCOUNT_ID.dkr.ecr.<AWS_REGION>.amazonaws.com/genomes-in-the-cloud:2.4.7-1603303710"
}

``
Do you have any suggestion on how to update this parameter-input.json for the reference fasta ("ref_fasta") which is stored in the Reference Store

omics:us-east-1:account_ID:referenceStore/3242349265/reference/8625408453

[djemec]

similar to a sequence, you can reference a reference store file using:
omics://account-id.storage.region.amazonaws.com/reference-store-id/reference/reference-id/source or
omics://account-id.storage.region.amazonaws.com/reference-store-id/reference/reference-id/index