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template.json
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{
"MitochondriaPipeline.wgs_aligned_input_bam_or_cram": "/mnt/data2/wgs-short-read/crams/cram_goes_here",
"MitochondriaPipeline.wgs_aligned_input_bam_or_cram_index": "/mnt/data2/wgs-short-read/crams/crai_goes_here",
"MitochondriaPipeline.ref_fasta": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.fasta",
"MitochondriaPipeline.ref_dict": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.dict",
"MitochondriaPipeline.ref_fasta_index": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.fasta.fai",
"MitochondriaPipeline.mt_dict": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.dict",
"MitochondriaPipeline.mt_fasta": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.fasta",
"MitochondriaPipeline.mt_fasta_index": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.fasta.fai",
"MitochondriaPipeline.mt_amb": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.fasta.amb",
"MitochondriaPipeline.mt_ann": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.fasta.ann",
"MitochondriaPipeline.mt_bwt": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.fasta.bwt",
"MitochondriaPipeline.mt_pac": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.fasta.pac",
"MitochondriaPipeline.mt_sa": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.fasta.sa",
"MitochondriaPipeline.blacklisted_sites": "/mnt/data1/tools/mitochondria_m2_wdl/ref/blacklist_sites.hg38.chrM.bed",
"MitochondriaPipeline.blacklisted_sites_index": "/mnt/data1/tools/mitochondria_m2_wdl/ref/blacklist_sites.hg38.chrM.bed.idx",
"MitochondriaPipeline.mt_shifted_dict": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.dict",
"MitochondriaPipeline.mt_shifted_fasta": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta",
"MitochondriaPipeline.mt_shifted_fasta_index": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.fai",
"MitochondriaPipeline.mt_shifted_amb": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.amb",
"MitochondriaPipeline.mt_shifted_ann": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.ann",
"MitochondriaPipeline.mt_shifted_bwt": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.bwt",
"MitochondriaPipeline.mt_shifted_pac": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.pac",
"MitochondriaPipeline.mt_shifted_sa": "/mnt/data1/tools/mitochondria_m2_wdl/ref/Homo_sapiens_assembly38.chrM.shifted_by_8000_bases.fasta.sa",
"MitochondriaPipeline.shift_back_chain": "/mnt/data1/tools/mitochondria_m2_wdl/ref/ShiftBack.chain",
"MitochondriaPipeline.control_region_shifted_reference_interval_list": "/mnt/data1/tools/mitochondria_m2_wdl/ref/control_region_shifted.chrM.interval_list",
"MitochondriaPipeline.non_control_region_interval_list": "/mnt/data1/tools/mitochondria_m2_wdl/ref/non_control_region.chrM.interval_list"
}