# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "find_concatenate"
description: A module for concatenation of gzipped or uncompressed files getting around
  UNIX terminal argument size
keywords:
  - concatenate
  - gzip
  - cat
  - find
  - pigz
tools:
  - find:
      description: GNU find searches the directory tree rooted at each given starting-point
        by evaluating the given expression
      documentation: https://man7.org/linux/man-pages/man1/find.1.html
      licence: ["GPL-3.0-or-later"]
      identifier: ""
  - pigz:
      description: pigz, which stands for Parallel Implementation of GZip, is a fully
        functional replacement for gzip that exploits multiple processors and multiple
        cores to the hilt when compressing data.
      documentation: https://man7.org/linux/man-pages/man1/find.1.html
      licence: ["other"]
      identifier: ""

input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - files_in:
        type: file
        description: List of either compressed or uncompressed files
        pattern: "*"
        ontologies: []
output:
  file_out:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}:
          type: file
          description: Concatenated file. Will be gzipped if ${prefix} ends with ".gz"
            or inputs are gzipped, will be uncompressed otherwise.
          pattern: "${file_out}"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"

        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@BioWilko"
maintainers:
  - "@BioWilko"
