nf-core_modules/software/subread/featurecounts/meta.yml

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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: "*.{version.txt}"
authors:
- "@ntoda03"