name: "rtgtools_format"
description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into the RTG Sequence Data File (SDF) format.
keywords:
  - rtg
  - fasta
  - fastq
  - bam
  - sam
tools:
  - "rtgtools":
      description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation"
      homepage: "https://www.realtimegenomics.com/products/rtg-tools"
      documentation: "https://github.com/RealTimeGenomics/rtg-tools"
      tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
      licence: "['BSD']"
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input1:
      type: file
      description: FASTA, FASTQ, BAM or SAM file. This should be the left input file when using paired end FASTQ/FASTA data
      pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}"
  - input2:
      type: file
      description: The right input file when using paired end FASTQ/FASTA data
      pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}"
  - sam_rg:
      type: file
      description: A file containing a single readgroup header as a SAM header. This can also be supplied as a string in `task.ext.args` as `--sam-rg <rg_line>`.
      pattern: "*.{txt,sam}"
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"
  - sdf:
      type: directory
      description: The sequence dictionary format folder created from the input file(s)
      pattern: "*.sdf"
authors:
  - "@nvnieuwk"
maintainers:
  - "@nvnieuwk"
