bcftools:
  bcftools_index:
    ft: ['.vcf.gz']
  bcftools_isec:
    ft: ['.vcf.gz']
  bcftools_stats:
    ft: ['.vcf.gz']

bedtools:
  bedtools_coverage:
    ft: ['.bed', '.bam']
    output: [PUR.HG00731.tiny.sort.bam.coverage10.bed]
  bedtools_min_genomecov:
    ft: ['.bam']
    output: [PUR.HG00731.tiny.sort.bam.10.coverage.bed]

bowtie:
  bowtie_build:
    ft: ['.fa']
    output: ['scaffolds.fa.1.ebwt']

bowtie2:
  bowtie2_build:
    ft: ['.fa']
    output: ['scaffolds.fa.1.bt2']

    
picard:
  picard_add_or_replace_read_groups:
    ft: ['config', 'sampleinfo']
  picard_bed_to_interval_list:
    ft: ['sampleinfo']
  picard_calculate_hs_metrics:
    ft: ['sampleinfo']
  picard_collect_insert_size_metrics:
    ft: ['sampleinfo']
  picard_collect_alignment_summary_metrics:
    ft: ['sampleinfo']
  

Add config file for input configuration
Add config file for input configuration
