nf-core_modules/modules/mtnucratio/meta.yml

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name: mtnucratio
description: A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.
keywords:
- mtnucratio
- ratio
- reads
- bam
- mitochondrial to nuclear ratio
- mitochondria
- statistics
tools:
- mtnucratio:
description: A small tool to determine MT to Nuclear ratios for NGS data.
homepage: https://github.com/apeltzer/MTNucRatioCalculator
documentation: https://github.com/apeltzer/MTNucRatioCalculator
tool_dev_url: https://github.com/apeltzer/MTNucRatioCalculator
doi: "10.1186/s13059-016-0918-z"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: (coordinate) sorted BAM/SAM file
pattern: "*.{bam,sam}"
- mt_id:
type: string
description: Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- mtnucratio:
type: file
description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)
pattern: "*.mtnucratio"
- json:
type: file
description: JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file
pattern: "*.json"
authors:
- "@louperelo"