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']

input:
  - meta:
      type: map
      description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/SAM file containing read alignments
      pattern: "*.{bam}"
  - annotation:
      type: file
      description: Genomic features annotation in GTF or SAF
      pattern: "*.{gtf,saf}"

output:
  - meta:
      type: map
      description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
  - counts:
      type: file
      description: Counts of reads mapping to features
      pattern: "*featureCounts.txt"
  - summary:
      type: file
      description: Summary log file
      pattern: "*.featureCounts.txt.summary"
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"

authors:
  - "@ntoda03"