You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
64 lines
1.7 KiB
YAML
64 lines
1.7 KiB
YAML
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"
|