---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "bwamem2decontnobams"
description: Decontamination module using bwamem2 and samtools that generates fastq files on the fly
keywords:
  - alignment
  - decontamination
  - fastq
tools:
  - bwamem2:
      description: "Mapping DNA sequences against a large reference genome"
      tool_dev_url: "https://github.com/bwa-mem2/bwa-mem2"
  - samtools:
      description: "Tools for dealing with SAM, BAM and CRAM files"
      documentation: "http://www.htslib.org/doc/1.1/samtools.html"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'sample1', single_end:false ]`
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2
        for single-end and paired-end data, respectively
  - meta2:
      type: map
      description: |
        Groovy Map containing reference genome information
        e.g. [ id:'ref_name' ]
  - index:
      type: file
      description: |
        A list of BWA index files

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. `[ id:'sample1', single_end:false ]`
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - decont_reads:
      type: file
      description: |
        List of fastq files. Two files for paired-end reads and one file for single-end reads

authors:
  - "@EBI-metagenomics"
maintainers:
  - "@EBI-metagenomics"
