mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
4619d012e5
* Add CRAM support to allelecounter * Update meta.yml * Rename bam,bai to input,input_index * Apply suggestions from code review * Fix reference to renamed variable Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
55 lines
1.4 KiB
YAML
55 lines
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"
|