nf-core_modules/modules/bedtools/genomecov/meta.yml

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name: bedtools_genomecov
description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.
keywords:
- bed
- bam
- genomecov
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- intervals:
type: file
description: BAM/BED/GFF/VCF
pattern: "*.{bam|bed|gff|vcf}"
- scale:
type: value
description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
- sizes:
type: file
description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
- extension:
type: string
description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- genomecov:
type: file
description: Computed genome coverage file
pattern: "*.${extension}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"
- "@sruthipsuresh"
- "@drpatelh"
- "@sidorov-si"
- "@chris-cheshire"