mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
55 lines
1.6 KiB
YAML
55 lines
1.6 KiB
YAML
|
name: mobsuite_recon
|
||
|
|
description: A tool to reconstruct plasmids in bacterial assemblies
|
||
|
|
keywords:
|
||
|
|
- bacteria
|
||
|
|
- plasmid
|
||
|
|
tools:
|
||
|
|
- mobsuite:
|
||
|
|
description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
|
||
|
|
homepage: https://github.com/phac-nml/mob-suite
|
||
|
|
documentation: https://github.com/phac-nml/mob-suite
|
||
|
|
tool_dev_url: https://github.com/phac-nml/mob-suite
|
||
|
|
doi: "10.1099/mgen.0.000435"
|
||
|
|
licence: ['Apache License, Version 2.0']
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- fasta:
|
||
|
|
type: file
|
||
|
|
description: A bacterial genome assembly in FASTA format
|
||
|
|
pattern: "*.{fasta,fa,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"
|
||
|
|
- chromosome:
|
||
|
|
type: file
|
||
|
|
description: FASTA file of all contigs found to belong to the chromosome
|
||
|
|
pattern: "chromosome.fasta"
|
||
|
|
- contig_report:
|
||
|
|
type: file
|
||
|
|
description: Assignment of the contig to chromosome or a particular plasmid grouping
|
||
|
|
pattern: "contig_report.txt"
|
||
|
|
- plasmids:
|
||
|
|
type: file
|
||
|
|
description: Each plasmid group is written to an individual FASTA
|
||
|
|
pattern: "plasmid_*.fasta"
|
||
|
|
- mobtyper_results:
|
||
|
|
type: file
|
||
|
|
description: Aggregate MOB-typer report files for all identified plasmid
|
||
|
|
pattern: "mobtyper_results.txt"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@rpetit3"
|