mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 14:13:09 +00:00
839bc6b1ad
* not yet working: add db version to versions.yml * next try: db version number not in versions.yml * Fix amrfinderplus versioning * Update main.nf * Apply suggestions from code review * Update main.nf * Dump version for syncrony with run * Update test.yml * Apply suggestions from code review * add tool and db version to output * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update meta.yml Co-authored-by: James Fellows Yates <jfy133@gmail.com>
59 lines
1.8 KiB
YAML
59 lines
1.8 KiB
YAML
name: amrfinderplus_run
|
|
description: Identify antimicrobial resistance in gene or protein sequences
|
|
keywords:
|
|
- bacteria
|
|
- fasta
|
|
- antibiotic resistance
|
|
tools:
|
|
- amrfinderplus:
|
|
description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
|
|
homepage: https://github.com/ncbi/amr/wiki
|
|
documentation: https://github.com/ncbi/amr/wiki
|
|
tool_dev_url: https://github.com/ncbi/amr
|
|
doi: "10.1038/s41598-021-91456-0"
|
|
licence: ["Public Domain"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- fasta:
|
|
type: file
|
|
description: Nucleotide or protein sequences in FASTA format
|
|
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
|
|
- db:
|
|
type: file
|
|
description: A compressed tarball of the AMRFinderPlus database to query
|
|
pattern: "*.tar.gz"
|
|
|
|
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"
|
|
- report:
|
|
type: file
|
|
description: AMRFinder+ final report
|
|
pattern: "*.tsv"
|
|
- mutation_report:
|
|
type: file
|
|
description: Report of organism-specific point-mutations
|
|
pattern: "*-mutations.tsv"
|
|
- tool_version:
|
|
type: string
|
|
description: The version of the tool in string format (useful for downstream tools such as hAMRronization)
|
|
- db_version:
|
|
type: string
|
|
description: The version of the used database in string format (useful for downstream tools such as hAMRronization)
|
|
|
|
authors:
|
|
- "@rpetit3"
|
|
- "@louperelo"
|
|
- "@jfy133"
|