# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: bam_stats_samtools
description: Produces comprehensive statistics from SAM/BAM/CRAM file
keywords:
  - statistics
  - counts
  - bam
  - sam
  - cram
modules:
  - samtools/stats
  - samtools/idxstats
  - samtools/flagstat
input:
  - ch_bam_bai:
      description: |
        The input channel containing the BAM/CRAM and it's index
        Structure: [ val(meta), path(bam), path(bai) ]
  - ch_fasta:
      description: |
        Reference genome fasta file
        Structure: [ path(fasta) ]
output:
  - stats:
      description: |
        File containing samtools stats output
        Structure: [ val(meta), path(stats) ]
  - flagstat:
      description: |
        File containing samtools flagstat output
        Structure: [ val(meta), path(flagstat) ]
  - idxstats:
      description: |
        File containing samtools idxstats output
        Structure: [ val(meta), path(idxstats)]
  - versions:
      description: |
        Files containing software versions
        Structure: [ path(versions.yml) ]
authors:
  - "@drpatelh"
