.
    ├── check_TB_coverage       				# TB whole genome / Amplicon coverage
    │   ├── bam 									# alignement of different samples mapped to H37Rv
    │   └── Coverage 								# coverage
    │       ├── 12_AMP*.moddepth.region.bed.gz 		# coverage at TB whole genome
    │       └── 12_AMR*.moddepth.region.bed.gz 		# coverage at Amplicon regions
    ├── variant_alling							# Variant calling results
    │   ├── vcf_truth 								# Truth variants set
    │   │   ├── tb_bcg_mexico.fa					# Genome of NC_016804.1
    │   │   └── Mycobacterium*.vcf              	# H37Rv variants in NC_016804.1
    │   ├── bam 									# alignement of different samples mapped to NC_016804.1
    │   ├── Control 								# variant calling results for control run
    │   │   ├── benchmark_whole_tb					# benchmark results at whole TB genome
    │   │   ├── benchmark_amplicon_regions			# benchmark results at Amplicon regions
    │   │   └── ...                 
    │   ├── readfish								# variant calling results for readfish run
    │   │   └── ...                 
    │   ├── UNCALLED 								# variant calling results for UNCALLED run
    │   │   └── ...                 
    │   └── Amplicon								# variant calling results for Amplicon run
    │       └── ...                 
    ├── workflow_output                         # ONT-TB_NF output for all samples
    │   └── ...                 
    └── fast5 									# FAST5 files for sequenced samples
    	└── ...