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input_template.json
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{
"MitochondriaPipeline.wgs_aligned_input_bam_or_cram": "",
"MitochondriaPipeline.wgs_aligned_input_bam_or_cram_index": "",
"MitochondriaPipeline.mt_shifted_fasta": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta",
"MitochondriaPipeline.mt_shifted_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.fai",
"MitochondriaPipeline.mt_fasta": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta",
"MitochondriaPipeline.mt_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.fai",
"MitochondriaPipeline.mt_bwt": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.bwt",
"MitochondriaPipeline.mt_amb": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.amb",
"MitochondriaPipeline.mt_dict": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.dict",
"MitochondriaPipeline.mt_ann": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.ann",
"MitochondriaPipeline.mt_pac": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.pac",
"MitochondriaPipeline.mt_sa": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.fasta.sa",
"MitochondriaPipeline.mt_shifted_bwt": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt",
"MitochondriaPipeline.mt_shifted_amb": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.amb",
"MitochondriaPipeline.mt_shifted_dict": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.dict",
"MitochondriaPipeline.mt_shifted_ann": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.ann",
"MitochondriaPipeline.mt_shifted_pac": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac",
"MitochondriaPipeline.mt_shifted_sa": "gs://gcp-public-data--broad-references/hg38/v0/chrM/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa",
"MitochondriaPipeline.blacklisted_sites": "gs://gcp-public-data--broad-references/hg38/v0/chrM/blacklist_sites.hg38.chrM.bed",
"MitochondriaPipeline.blacklisted_sites_index": "gs://gcp-public-data--broad-references/hg38/v0/chrM/blacklist_sites.hg38.chrM.bed.idx",
"MitochondriaPipeline.control_region_shifted_reference_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/chrM/control_region_shifted.chrM.interval_list",
"MitochondriaPipeline.shift_back_chain": "gs://gcp-public-data--broad-references/hg38/v0/chrM/ShiftBack.chain",
"MitochondriaPipeline.non_control_region_interval_list": "gs://gatk-best-practices/mitochondria-pipeline/non_control_region.interval_list",
"MitochondriaPipeline.gatk_docker_override": "us.gcr.io/broad-gatk/gatk:4.5.0.0",
"MitochondriaPipeline.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"MitochondriaPipeline.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"MitochondriaPipeline.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai"
}