mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
62 lines
1.5 KiB
YAML
62 lines
1.5 KiB
YAML
|
name: cmseq_polymut
|
||
|
|
description: Calculates polymorphic site rates over protein coding genes
|
||
|
|
keywords:
|
||
|
|
- polymut
|
||
|
|
- polymorphic
|
||
|
|
- mags
|
||
|
|
- assembly
|
||
|
|
- polymorphic sites
|
||
|
|
- estimation
|
||
|
|
- protein coding genes
|
||
|
|
- cmseq
|
||
|
|
- bam
|
||
|
|
- coverage
|
||
|
|
tools:
|
||
|
|
- cmseq:
|
||
|
|
description: Set of utilities on sequences and BAM files
|
||
|
|
homepage: https://github.com/SegataLab/cmseq
|
||
|
|
documentation: https://github.com/SegataLab/cmseq
|
||
|
|
tool_dev_url: https://github.com/SegataLab/cmseq
|
||
|
|
licence: ['MIT License']
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- bam:
|
||
|
|
type: file
|
||
|
|
description: BAM file
|
||
|
|
pattern: "*.bam"
|
||
|
|
- bai:
|
||
|
|
type: file
|
||
|
|
description: BAM index file
|
||
|
|
pattern: "*.bai"
|
||
|
|
- gff:
|
||
|
|
type: file
|
||
|
|
description: GFF file used to extract protein-coding genes
|
||
|
|
pattern: "*.gff"
|
||
|
|
- fasta:
|
||
|
|
type: file
|
||
|
|
description: Optional fasta file to run on a subset of references in the BAM file.
|
||
|
|
pattern: .{fa,fasta,fas,fna}
|
||
|
|
|
||
|
|
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"
|
||
|
|
- polymut:
|
||
|
|
type: file
|
||
|
|
description: Polymut report in `.txt` format.
|
||
|
|
pattern: "*.txt"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@maxibor"
|