Nextflow Registry | nf-core/resfinder/run@0.0.0-6c4ed3a

nf-core/resfinder/run @ 0.0.0-6c4ed3a

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria

blastn kma microbes resfinder resistance genes

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @marrip

Maintainers: @marrip

ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria

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

include { RESFINDER_RUN } from 'nf-core/resfinder/run'

MIT License

Process

`Name`	`RESFINDER_RUN`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fastq` file	fastq file(s) `*.{fastq,fq}{.gz}`
`fasta` file	fasta file `*.{fa,fna}`

`db_point` directory	database directory containing known point mutations

`db_res` directory	database directory containing known resistance genes

Output 16 channels

#1 json tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.json` file	CGE standardized json file `*.json`

#2 versions

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

#3 pheno_table tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`pheno_table.txt` file	table with all AMR phenotypes `pheno_table.tsv`

#4 resfinder_kma tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`resfinder_kma` directory	directory holding kma results `resfinder_kma`

#5 disinfinder_kma tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`disinfinder_kma` directory	directory holding kma results `disinfinder_kma`

#6 pointfinder_kma tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`pointfinder_kma` directory	directory holding kma results `pointfinder_kma`

#7 resfinder_blast tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`resfinder_blast` directory	directory holding blast results `resfinder_kma`

#8 pointfinder_table tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`PointFinder_table.txt` file	predicted point mutations grouped into genes to which they belong `PointFinder_table.txt`

#9 resfinder_results tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`ResFinder_results.txt` file	predicted resistance genes grouped by antibiotic class and hit alignments to reference resistance genes `ResFinder_results.txt`

#10 pheno_table_species tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`pheno_table_species.txt` file	table with species specific AMR phenotypes `pheno_table_species.tsv`

#11 pointfinder_results tuple