nf-core_modules/modules/macs2/callpeak/meta.yml

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name: macs2_callpeak
description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
keywords:
- alignment
- atac-seq
- chip-seq
- peak-calling
tools:
- macs2:
description: Model Based Analysis for ChIP-Seq data
homepage: None
documentation: https://docs.csc.fi/apps/macs2/
tool_dev_url: https://github.com/macs3-project/MACS
doi: "https://doi.org/10.1101/496521"
licence: ["BSD"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- ipbam:
type: file
description: The ChIP-seq treatment file
- controlbam:
type: file
description: The control file
- macs2_gsize:
type: string
description:
Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)
output:
- versions:
type: file
description: File containing software version
pattern: "versions.yml"
- peak:
type: file
description: BED file containing annotated peaks
pattern: "*.gappedPeak,*.narrowPeak}"
- xls:
type: file
description: xls file containing annotated peaks
pattern: "*.xls"
- gapped:
type: file
description: Optional BED file containing gapped peak
pattern: "*.gappedPeak"
- bed:
type: file
description: Optional BED file containing peak summits locations for every peak
pattern: "*.bed"
- bdg:
type: file
description: Optional bedGraph files for input and treatment input samples
pattern: "*.bdg"
authors:
- "@ntoda03"
- "@JoseEspinosa"
- "@jianhong"