Update links to use public containers with HTTP links
This commit is contained in:
Matt McLoughlin
GitHub
Коммит
aadcac3a16
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@ -1,6 +1,6 @@
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{
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"WorkflowUrl":"https://raw.githubusercontent.com/microsoft/gatk4-data-processing-azure/az1.1.0/processing-for-variant-discovery-gatk4.wdl",
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"WorkflowInputsUrl":"https://raw.githubusercontent.com/microsoft/gatk4-data-processing-azure/az1.1.0/processing-for-variant-discovery-gatk4.b37.wgs.inputs.json",
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"WorkflowUrl":"https://raw.githubusercontent.com/microsoft/gatk4-data-processing-azure/main-azure/processing-for-variant-discovery-gatk4.wdl",
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"WorkflowInputsUrl":"https://raw.githubusercontent.com/microsoft/gatk4-data-processing-azure/main-azure/processing-for-variant-discovery-gatk4.b37.wgs.inputs.json",
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"WorkflowOptionsUrl":null,
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"WorkflowDependenciesUrl":null
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}
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@ -2,27 +2,27 @@
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"##_COMMENT1": "SAMPLE NAME AND UNMAPPED BAMS",
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"PreProcessingForVariantDiscovery_GATK4.sample_name": "NA12878",
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"PreProcessingForVariantDiscovery_GATK4.ref_name": "b37",
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"PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list": "/datasettestinputs/dataset/gatk4-data-processing/NA12878_downsampled_for_testing/unmapped/NA12878_downsampled.txt",
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"PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list": "https://datasettestinputs.blob.core.windows.net/dataset/gatk4-data-processing/NA12878_downsampled_for_testing/unmapped/NA12878_downsampled.txt",
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"PreProcessingForVariantDiscovery_GATK4.unmapped_bam_suffix": ".bam",
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"##_COMMENT2": "REFERENCE FILES",
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"PreProcessingForVariantDiscovery_GATK4.ref_dict": "/datasettestinputs/dataset/references/b37/human_g1k_v37_decoy.dict",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta": "/datasettestinputs/dataset/references/b37/human_g1k_v37_decoy.fasta",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta_index": "/datasettestinputs/dataset/references/b37/human_g1k_v37_decoy.fasta.fai",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_sa": "/datasettestinputs/dataset/references/b37/human_g1k_v37_decoy.fasta.sa",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_amb": "/datasettestinputs/dataset/references/b37/human_g1k_v37_decoy.fasta.amb",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_bwt": "/datasettestinputs/dataset/references/b37/human_g1k_v37_decoy.fasta.bwt",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_ann": "/datasettestinputs/dataset/references/b37/human_g1k_v37_decoy.fasta.ann",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_pac": "/datasettestinputs/dataset/references/b37/human_g1k_v37_decoy.fasta.pac",
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"PreProcessingForVariantDiscovery_GATK4.ref_dict": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.dict",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta_index": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.fai",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_sa": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.sa",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_amb": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.amb",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_bwt": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.bwt",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_ann": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.ann",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_pac": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/human_g1k_v37_decoy.fasta.pac",
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"##_COMMENT3": "KNOWN SITES RESOURCES",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf": "/datasettestinputs/dataset/references/b37/dbsnp_138.b37.vcf",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "/datasettestinputs/dataset/references/b37/dbsnp_138.b37.vcf.idx",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/dbsnp_138.b37.vcf",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "https://datasettestinputs.blob.core.windows.net/dataset/references/b37/dbsnp_138.b37.vcf.idx",
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"PreProcessingForVariantDiscovery_GATK4.known_indels_sites_VCFs": [
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"/datasettestinputs/dataset/references/b37/Mills_and_1000G_gold_standard.indels.b37.vcf"
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"https://datasettestinputs.blob.core.windows.net/dataset/references/b37/Mills_and_1000G_gold_standard.indels.b37.vcf"
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],
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"PreProcessingForVariantDiscovery_GATK4.known_indels_sites_indices": [
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"/datasettestinputs/dataset/references/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx"
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"https://datasettestinputs.blob.core.windows.net/dataset/references/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx"
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],
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"##_COMMENT4": "MISC PROGRAM PARAMETERS",
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{
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"WorkflowUrl":"https://raw.githubusercontent.com/microsoft/gatk4-data-processing-azure/az1.1.0/processing-for-variant-discovery-gatk4.wdl",
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"WorkflowInputsUrl":"https://raw.githubusercontent.com/microsoft/gatk4-data-processing-azure/az1.1.0/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json",
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"WorkflowUrl":"https://raw.githubusercontent.com/microsoft/gatk4-data-processing-azure/main-azure/processing-for-variant-discovery-gatk4.wdl",
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"WorkflowInputsUrl":"https://raw.githubusercontent.com/microsoft/gatk4-data-processing-azure/main-azure/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json",
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"WorkflowOptionsUrl":null,
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"WorkflowDependenciesUrl":null
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}
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@ -2,30 +2,30 @@
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"##_COMMENT1": "SAMPLE NAME AND UNMAPPED BAMS",
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"PreProcessingForVariantDiscovery_GATK4.sample_name": "NA12878",
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"PreProcessingForVariantDiscovery_GATK4.ref_name": "hg38",
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"PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list": "/datasettestinputs/dataset/gatk4-data-processing/NA12878_downsampled_for_testing/unmapped/NA12878_downsampled.txt",
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"PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list": "https://datasettestinputs.blob.core.windows.net/dataset/gatk4-data-processing/NA12878_downsampled_for_testing/unmapped/NA12878_downsampled.txt",
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"PreProcessingForVariantDiscovery_GATK4.unmapped_bam_suffix": ".bam",
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"##_COMMENT2": "REFERENCE FILES",
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"PreProcessingForVariantDiscovery_GATK4.ref_dict": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.dict",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta_index": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_alt": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_sa": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_amb": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_bwt": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_ann": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_pac": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
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"PreProcessingForVariantDiscovery_GATK4.ref_dict": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.dict",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta",
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"PreProcessingForVariantDiscovery_GATK4.ref_fasta_index": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_alt": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_sa": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_amb": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_bwt": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_ann": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
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"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_pac": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac",
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"##_COMMENT3": "KNOWN SITES RESOURCES",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
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"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
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"PreProcessingForVariantDiscovery_GATK4.known_indels_sites_VCFs": [
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"/datasettestinputs/dataset/references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
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"/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"
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"https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
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"https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"
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],
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"PreProcessingForVariantDiscovery_GATK4.known_indels_sites_indices": [
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"/datasettestinputs/dataset/references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
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"/datasettestinputs/dataset/references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
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"https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
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"https://datasettestinputs.blob.core.windows.net/dataset/references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
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],
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"##_COMMENT4": "MISC PARAMETERS",
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