name: sentieon_datametrics
description: Collects multiple quality metrics from a bam file
keywords:
  - metrics
  - bam
  - sentieon
tools:
  - sentieon:
      description: |
        Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads.
        Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.
      homepage: https://www.sentieon.com/
      documentation: https://www.sentieon.com/
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - meta3:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - bam:
      type: file
      description: Sorted BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - bai:
      type: file
      description: Index of th sorted BAM/CRAM/SAM file
      pattern: "*.{bai,crai,sai}"
  - fasta:
      type: file
      description: Genome fasta file
      pattern: "*.{fa,fasta}"
  - fai:
      type: file
      description: Index of the genome fasta file
      pattern: "*.fai"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'test', single_end:false ]`
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - mq_metrics:
      type: file
      description: File containing the information about mean base quality score for each sequencing cycle
      pattern: "*.txt"
  - qd_metrics:
      type: file
      description: File containing the information about number of bases with a specific base quality score
      pattern: "*.txt"
  - gc_summary:
      type: file
      description: File containing the information about GC bias in the reference and the sample
      pattern: "*.txt"
  - gc_metrics:
      type: file
      description: File containing the information about GC bias in the reference and the sample
      pattern: "*.txt"
  - aln_metrics:
      type: file
      description: File containing the statistics about the alignment of the reads
      pattern: "*.txt"
  - is_metrics:
      type: file
      description: File containing the information about statistical distribution of insert sizes
      pattern: "*.txt"
authors:
  - "@ramprasadn"
maintainers:
  - "@ramprasadn"
