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Where do the test files reside for the dockerstore.org workflows?

rdbremelrdbremel Madison WIMember

**e.g.
JSON for RNAseq

rna-germline-variant-calling

the files are not FTPable and are not in the "bundle" directories
**

{
"##_COMMENT1": "Input",
"RNAseq.inputBam": "gs://gatk-test-data/rna_bam/NA12878_b37/NA12878.bam",

"##_COMMENT2": "REFERENCE FILES",
"RNAseq.refFasta": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta",
"RNAseq.refFastaIndex": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.fasta.fai",
"RNAseq.refDict": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dict",

"##_COMMENT3": "INTERVALS",
"RNAseq.wgsCallingIntervalList": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.whole_genome.interval_list",

"##_COMMENT4": "RESOURCE FILES",
"RNAseq.dbSnpVcf": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dbsnp138.vcf",
"RNAseq.dbSnpVcfIndex": "gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.dbsnp138.vcf.idx",
"RNAseq.knownVcfs": [
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Mills_and_1000G_gold_standard.indels.b37.sites.vcf",
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.known_indels.vcf"
],
"RNAseq.knownVcfsIndices": [
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx",
"gs://broad-references/Homo_sapiens_assembly19_1000genomes_decoy/Homo_sapiens_assembly19_1000genomes_decoy.known_indels.vcf.idx"
],
"RNAseq.annotationsGTF": "gs://gatk-test-data/intervals/star.gencode.v19.transcripts.patched_contigs.gtf",

"##_COMMENT4": "DOCKERS",
"#RNAseq.gatk4_docker_override": "String? (optional)",
"#RNAseq.star_docker_override": "String? (optional)",
"#RNAseq.gitc_docker_override": "String? (optional)",

"##_COMMENT5": "PATHS",
"#RNAseq.gatk_path_override": "/gatk/gatk",

"##_COMMENT6": "PREEMPTIBLES",
"##RNAseq.preemptible_tries": "(optional) Int?",

"##_COMMENT7": "Misc",
"#RNAseq.StarAlign.num_threads": "(optional) Int?",
"#RNAseq.StarAlign.star_limitOutSJcollapsed": "(optional) Int?",
"RNAseq.StarAlign.additional_disk": "50",
"#RNAseq.StarAlign.star_mem_max_gb": "(optional) Int?",
"RNAseq.StarGenerateReferences.addtional_disk": 50,
"#RNAseq.StarGenerateReferences.num_threads": "(optional) Int?",
"#RNAseq.StarGenerateReferences.mem_gb": "(optional) Int?",
"#RNAseq.haplotypeScatterCount": "(optional) Int?",
"#RNAseq.use_gatk4_for_all_tools": "(optional) Boolean",
"#RNAseq.minConfidenceForVariantCalling": "(optional) Int?",
"#RNAseq.zippedStarReferences": "(optional) File?",
"#RNAseq.readLength": "(optional) Int?"
}

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