name: "bam_dedup_stats_samtools_umitools"
description: UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats
keywords:
  - umi
  - dedup
  - index
  - bam
  - sam
  - cram
modules:
  - umitools/dedup
  - samtools/index
  - samtools/stats
  - samtools/idxstats
  - samtools/flagstat
input:
  - bam_bai:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - get_dedup_stats:
      type: boolean
      description: |
        Generate output stats when running "umi_tools dedup"
output:
  - bam:
      type: file
      description: Umi deduplicated BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - bai:
      type: file
      description: Umi deduplicated BAM/CRAM/SAM samtools index
      pattern: "*.{bai,crai,sai}"
  - csi:
      type: file
      description: CSI samtools index
      pattern: "*.csi"
  - stats:
      type: file
      description: File containing samtools stats output
      pattern: "*.{stats}"
  - flagstat:
      type: file
      description: File containing samtools flagstat output
      pattern: "*.{flagstat}"
  - idxstats:
      type: file
      description: File containing samtools idxstats output
      pattern: "*.{idxstats}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@drpatelh"
  - "@KamilMaliszArdigen"
