name: subread_featurecounts
description: Count reads that map to genomic features
keywords:
  - counts
  - fasta
  - genome
  - reference
tools:
  - featurecounts:
      description: featureCounts is a highly efficient general-purpose read summarization
        program that counts mapped reads for genomic features such as genes, exons,
        promoter, gene bodies, genomic bins and chromosomal locations. It can be used
        to count both RNA-seq and genomic DNA-seq reads.
      homepage: http://bioinf.wehi.edu.au/featureCounts/
      documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
      doi: "10.1093/bioinformatics/btt656"
      licence: ["GPL v3"]
      identifier: biotools:subread
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - bams:
        type: file
        description: BAM files containing mapped reads
        pattern: "*.bam"
        ontologies: []
    - annotation:
        type: file
        description: Genomic features annotation in GTF or SAF
        pattern: "*.{gtf,saf}"
        ontologies: []
output:
  counts:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*featureCounts.tsv":
          type: file
          description: Counts of reads mapping to features
          pattern: "*featureCounts.tsv"
          ontologies:
            - edam: http://edamontology.org/format_3475 # TSV
  summary:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*featureCounts.tsv.summary":
          type: file
          description: Summary log file
          pattern: "*.featureCounts.tsv.summary"
          ontologies: []
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@ntoda03"
maintainers:
  - "@ntoda03"
