nf-core_modules/modules/fargene/meta.yml

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name: fargene
description: tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.
keywords:
- antibiotic resistance genes
- ARGs
- identifier
- metagenomic
- contigs
tools:
- fargene:
description: Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output
homepage: https://github.com/fannyhb/fargene
documentation: https://github.com/fannyhb/fargene
tool_dev_url: https://github.com/fannyhb/fargene
doi: ""
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)
pattern: "*.{fasta}"
- hmm_model:
type: string
description: name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]
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"
- log:
type: file
description: log file
pattern: "*.{log}"
- txt:
type: file
description: analysis summary text file
pattern: "*.{txt}"
- hmm:
type: file
description: output from hmmsearch
pattern: "*.{out}"
- orfs:
type: file
description: open reading frames (ORFs)
pattern: "*.{fasta}"
- orfs_amino:
type: file
description: protein translation of open reading frames (ORFs)
pattern: "*.{fasta}"
- contigs:
type: file
description: (complete) contigs that passed the final full-length classification
pattern: "*.{fasta}"
- contigs_pept:
type: file
description: parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences
pattern: "*.{fasta}"
- filtered:
type: file
description: sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene
pattern: "*.{fasta}"
- filtered_pept:
type: file
description: sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located
pattern: "*.{fasta}"
- fragments:
type: file
description: All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files
pattern: "*.{fastq}"
- trimmed:
type: file
description: The quality controlled retrieved fragments from each input file.
pattern: "*.{fasta}"
- spades:
type: directory
description: The output from the SPAdes assembly
pattern: "spades_assembly"
- metagenome:
type: file
description: The FASTQ to FASTA converted input files from metagenomic reads.
pattern: "*.{fasta}"
- tmp:
type: file
description: The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used.
pattern: "*.{fasta}"
authors:
- "@louperelo"