modules/resfinder_run

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

blastnkmamicrobesresfinderresistance genes

https://github.com/nf-core/modules/[...]/modules/nf-core/resfinder/run

Description

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

Input

name:type

description

pattern

`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

name:type

description

pattern

`json`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`*.json:file`

CGE standardized json file

*.json

`disinfinder_kma`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`disinfinder_kma:directory`

directory holding kma results

disinfinder_kma

`pheno_table_species`

`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

`pheno_table`

`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

`pointfinder_kma`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`pointfinder_kma:directory`

directory holding kma results

pointfinder_kma

`pointfinder_prediction`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`PointFinder_prediction.txt:file`

tab separated table; 1 is given to a predicted resistance against an antibiotic class, 0 is given to not resistance detected

PointFinder_prediction.txt

`pointfinder_results`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`PointFinder_results.txt:file`

tab separated table with predicted point mutations leading to antibiotic resistance

PointFinder_results.txt

`pointfinder_table`

`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

`resfinder_hit_in_genome_seq`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`ResFinder_Hit_in_genome_seq.fsa:file`

fasta sequence of resistance gene hits found in the input data (query)

ResFinder_Hit_in_genome_seq.fsa

`resfinder_blast`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`resfinder_blast:directory`

directory holding blast results

resfinder_kma

`resfinder_kma`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`resfinder_kma:directory`

directory holding kma results

resfinder_kma

`resfinder_resistance_gene_seq`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`ResFinder_Resistance_gene_seq.fsa:file`

fasta sequence of resistance gene hits found in the database (reference)

ResFinder_Resistance_gene_seq.fsa

`resfinder_results_table`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`ResFinder_results_table.txt:file`

predicted resistance genes grouped by antibiotic class

ResFinder_results_table.txt

`resfinder_results_tab`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

`ResFinder_results_tab.txt:file`

tab separated table with predicted resistance genes

ResFinder_results_tab.txt

`resfinder_results`

`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

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

resfinder
APACHE-2.0

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

bitbucket.org/genomicepidemiology/resfinder.git/src bitbucket.org/genomicepidemiology/resfinder/src/master/README.md https://bitbucket.org/genomicepidemiology/resfinder.git/src 10.1099/mgen.0.000748

modules/resfinder_run

Description

Input

meta:map

fastq:file

fasta:file

db_point:directory

db_res:directory

Output

json

meta:map

*.json:file

disinfinder_kma

meta:map

disinfinder_kma:directory

pheno_table_species

meta:map

pheno_table_species.txt:file

pheno_table

meta:map

pheno_table.txt:file

pointfinder_kma

meta:map

pointfinder_kma:directory

pointfinder_prediction

meta:map

PointFinder_prediction.txt:file

pointfinder_results

meta:map

PointFinder_results.txt:file

pointfinder_table

meta:map

PointFinder_table.txt:file

resfinder_hit_in_genome_seq

meta:map

ResFinder_Hit_in_genome_seq.fsa:file

resfinder_blast

meta:map

resfinder_blast:directory

resfinder_kma

meta:map

resfinder_kma:directory

resfinder_resistance_gene_seq

meta:map

ResFinder_Resistance_gene_seq.fsa:file

resfinder_results_table

meta:map

ResFinder_results_table.txt:file

resfinder_results_tab

meta:map

ResFinder_results_tab.txt:file

resfinder_results

meta:map

ResFinder_results.txt:file

versions

versions.yml:file

Tools

resfinder APACHE-2.0

maintainer

get in touch

`meta:map`

`fastq:file`

`fasta:file`

`db_point:directory`

`db_res:directory`

`json`

`meta:map`

`*.json:file`

`disinfinder_kma`

`meta:map`

`disinfinder_kma:directory`

`pheno_table_species`

`meta:map`

`pheno_table_species.txt:file`

`pheno_table`

`meta:map`

`pheno_table.txt:file`

`pointfinder_kma`

`meta:map`

`pointfinder_kma:directory`

`pointfinder_prediction`

`meta:map`

`PointFinder_prediction.txt:file`

`pointfinder_results`

`meta:map`

`PointFinder_results.txt:file`

`pointfinder_table`

`meta:map`

`PointFinder_table.txt:file`

`resfinder_hit_in_genome_seq`

`meta:map`

`ResFinder_Hit_in_genome_seq.fsa:file`

`resfinder_blast`

`meta:map`

`resfinder_blast:directory`

`resfinder_kma`

`meta:map`

`resfinder_kma:directory`

`resfinder_resistance_gene_seq`

`meta:map`

`ResFinder_Resistance_gene_seq.fsa:file`

`resfinder_results_table`

`meta:map`

`ResFinder_results_table.txt:file`

`resfinder_results_tab`

`meta:map`

`ResFinder_results_tab.txt:file`

`resfinder_results`

`meta:map`

`ResFinder_results.txt:file`

`versions`

`versions.yml:file`

resfinder
APACHE-2.0