Nextflow Registry | nf-core/fargene@0.0.0-6c4ed3a

nf-core/fargene @ 0.0.0-6c4ed3a

tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.

antibiotic resistance genes ARGs identifier metagenomic contigs

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @louperelo

Maintainers: @louperelo

Summary

tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.

Get started

Add the following snippet to your workflow script to include this module.

include { FARGENE } from 'nf-core/fargene'

License

MIT License

Process

`Name`	`FARGENE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	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) `*.{fasta}`

`hmm_model` string	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 16 channels

#1 hmm tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/hmmsearchresults/*.out` file	output from hmmsearch (both single gene annotations + contigs) `*.{out}`

#2 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	log file `*.{log}`

#3 tmp tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/tmpdir/*.out` file	The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used. `*.{fasta}`

#4 txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/results_summary.txt` file	analysis summary text file `*.{txt}`

#5 orfs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/predictedGenes/predicted-orfs.fasta` file	open reading frames (ORFs) `*.{fasta}`

#6 spades tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/spades_assembly/*` directory	The output from the SPAdes assembly `spades_assembly`

#7 contigs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/predictedGenes/retrieved-contigs.fasta` file	(complete) contigs that passed the final full-length classification `*.{fasta}`

#8 trimmed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/retrievedFragments/trimmedReads/*.fasta` file	The quality controlled retrieved fragments from each input file. `*.{fasta}`

#9 filtered tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/predictedGenes/*filtered.fasta` file	sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene `*.{fasta}`

#10 versions

`versions.yml` file	File containing software versions `versions.yml`

#11 fragments tuple


`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]