nf-core_modules/modules/amrfinderplus/run/meta.yml
Edmund Miller f080015754
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https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358

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Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
2022-03-18 14:27:50 +01:00

51 lines
1.4 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"
authors:
- "@rpetit3"