nf-core_modules/modules/allelecounter/meta.yml
2022-04-14 13:35:01 +02:00

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1.4 KiB
YAML

name: allelecounter
description: Generates a count of coverage of alleles
keywords:
- allele
- count
tools:
- allelecounter:
description: Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings)
homepage: https://github.com/cancerit/alleleCount
documentation: https://github.com/cancerit/alleleCount
tool_dev_url: https://github.com/cancerit/alleleCount
doi: ""
licence: A-GPL 3.0
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- input_index:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- loci:
type: file
description: loci file <CHR><tab><POS1>
pattern: "*.{tsv}"
- fasta:
type: file
description: Input genome fasta file. Required when passing CRAM files.
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"
- alleleCount:
type: file
description: Allele count file
pattern: "*.{alleleCount}"
authors:
- "@fullama"
- "@fbdtemme"