nf-core_modules/modules/stadeniolib/scramble/meta.yml

name: "stadeniolib_scramble"
description: Advanced sequence file format conversions
keywords:
  - sam
  - bam
  - cram
  - compression
tools:
  - "scramble":
      description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats."
      homepage: "https://github.com/jkbonfield/io_lib"
      documentation: "https://github.com/jkbonfield/io_lib/blob/master/README.md"
      tool_dev_url: "https://github.com/jkbonfield/io_lib"
      licence: "['BSD']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - fasta:
      type: file
      description: Reference genome in FASTA format
      pattern: "*.{fa,fasta}"
  - fai:
      type: file
      description: FASTA index file from samtools faidx
      pattern: "*.{fai}"
  - gzi:
      type: file
      description: Optional gzip index file for BAM inputs
      pattern: "*.gzi"

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"
  - reads:
      type: file
      description: Converted reads
      pattern: "*.{sam, bam, cram}"
  - gzi:
      type: Optional file
      description: gzip index file for BAM outputs
      pattern: ".{bam.gzi}"
authors:
  - "@matthdsm"