nf-core_modules/modules/deeparg/predict/meta.yml
James A. Fellows Yates c3bacb9fdd
Add deeparg (#1234)
* Add deeparg download data

* Tweak downloaddata test.yml

* Add deeparg tests

* Apply suggestions from code review

* Fix output file paths in test

* Fix tests again md5sum to string
2022-01-26 15:19:16 +01:00

68 lines
2.1 KiB
YAML

name: deeparg_predict
description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
keywords:
- deeparg
- antimicrobial resistance
- antimicrobial resistance genes
- arg
- deep learning
- prediction
- contigs
- metagenomes
tools:
- deeparg:
description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
homepage: https://bench.cs.vt.edu/deeparg
documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
doi: "10.1186/s40168-018-0401-z"
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- fasta:
type: file
description: FASTA file containing gene-like sequences
pattern: "*.{fasta,fa,fna}"
- model:
type: string
description: Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively
pattern: "LS|LS"
- db:
type: directory
description: Path to a directory containing the deepARG pre-built models
pattern: "*/"
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"
- daa:
type: file
description: Sequences of ARG-like sequences from DIAMOND alignment
pattern: "*.align.daa"
- daa_tsv:
type: file
description: Alignments scores against ARG-like sequences from DIAMOND alignment
pattern: "*.align.daa.tsv"
- arg:
type: file
description: Table containing sequences with an ARG-like probability of more than specified thresholds
pattern: "*.mapping.ARG"
- potential_arg:
type: file
description: Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection
pattern: "*.mapping.potential.ARG"
authors:
- "@jfy133"