nf-core-modules/modules/nf-core/bwamem2/mem/meta.yml at 869d8058699b9e3b786648c357898fad7388c25f · nvnieuwk/nf-core-modules · GitHub

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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: bwamem2_mem
description: Performs fastq alignment to a fasta reference using BWA
keywords:
  - mem
  - bwa
  - alignment
  - map
  - fastq
  - bam
  - sam
tools:
  - bwa:
      description: |
        BWA-mem2 is a software package for mapping DNA sequences against
        a large reference genome, such as the human genome.
      homepage: https://github.com/bwa-mem2/bwa-mem2
      documentation: http://www.htslib.org/doc/samtools.html
      arxiv: arXiv:1303.3997
      licence: ["MIT"]
      identifier: "biotools:bwa-mem2"
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', 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.
        ontologies:
          - edam: "http://edamontology.org/data_2044" # Sequence
          - edam: "http://edamontology.org/format_1930" # FASTQ
  - - meta2:
        type: map
        description: |
          Groovy Map containing reference/index information
          e.g. [ id:'test' ]
    - index:
        type: file
        description: BWA genome index files
        pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
        ontologies:
          - edam: "http://edamontology.org/data_3210" # Genome index
  - - meta3:
        type: map
        description: |
          Groovy Map containing reference information
          e.g. [ id:'genome' ]
    - fasta:
        type: file
        description: Reference genome in FASTA format
        pattern: "*.{fa,fasta,fna}"
        ontologies:
          - edam: "http://edamontology.org/data_2044" # Sequence
          - edam: "http://edamontology.org/format_1929" # FASTA
  - sort_bam:
      type: boolean
      description: use samtools sort (true) or samtools view (false)
      pattern: "true or false"
output:
  sam:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.sam":
          type: file
          description: Output SAM file containing read alignments
          pattern: "*.{sam}"
          ontologies:
            - edam: "http://edamontology.org/format_2573" # SAM
  bam:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.bam":
          type: file
          description: Output BAM file containing read alignments
          pattern: "*.{bam}"
          ontologies:
            - edam: "http://edamontology.org/format_2572" # BAM
  cram:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.cram":
          type: file
          description: Output CRAM file containing read alignments
          pattern: "*.{cram}"
          ontologies:
            - edam: "http://edamontology.org/format_3462" # CRAM
  crai:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.crai":
          type: file
          description: Index file for CRAM file
          pattern: "*.{crai}"
          ontologies: []
  csi:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.csi":
          type: file
          description: Index file for BAM file
          pattern: "*.{csi}"
          ontologies: []
  versions_bwamem2:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - bwa-mem2:
          type: string
          description: The tool name
      - bwa-mem2 version 2>&1 | tail -1:
          type: string
          description: The command used to generate the version of the tool
  versions_samtools:
    - - ${task.process}:
          type: string
          description: The process the versions were collected from
      - samtools:
          type: string
          description: The tool name
      - samtools --version 2>&1 | head -1 | sed 's/^.*samtools //':
          type: string
          description: The command used to generate the version of the tool
topics:
  - versions:
      - - process:
            type: string
            description: The process the versions were collected from
        - tool:
            type: string
            description: The tool name
        - version:
            type: string
            description: The version of the tool
authors:
  - "@maxulysse"
  - "@matthdsm"
maintainers:
  - "@maxulysse"
  - "@matthdsm"