nf-core_modules/software/seacr/callpeak/meta.yml
2021-01-05 10:18:11 +00:00

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name: seacr_callpeak
description: Call peaks using SEACR on sequenced reads in bedgraph format
keywords:
- peak-caller
- peaks
- bedgraph
- cut&tag
- cut&run
- chromatin
- seacr
tools:
- seacr:
description: |
SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
or chromatin profiling data in which background is dominated by "zeroes"
(i.e. regions with no read coverage).
homepage: https://github.com/FredHutch/SEACR
documentation: https://github.com/FredHutch/SEACR
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bedgraph:
type: file
description: |
The target bedgraph file from which the peaks will be calculated.
- ctrlbedgraph:
type: file
description: |
Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed file containing the calculated peaks.
pattern: "*.bed"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@chris-cheshire"