Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

fastq{:bash}

:file

fastq file(s)

*.{fastq,fq}{.gz}

fasta{:bash}

:file

fasta file

*.{fa,fna}

db_point{:bash}

:directory

database directory containing known point mutations

db_res{:bash}

:directory

database directory containing known resistance genes

Output

name:type
description
pattern

json{:bash}

meta{:bash}

:map

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

*.json{:bash}

:file

CGE standardized json file

*.json

disinfinder_kma{:bash}

meta{:bash}

:map

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

disinfinder_kma{:bash}

:directory

directory holding kma results

disinfinder_kma

pheno_table_species{:bash}

meta{:bash}

:map

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

pheno_table_species.txt{:bash}

:file

table with species specific AMR phenotypes

pheno_table_species.tsv

pheno_table{:bash}

meta{:bash}

:map

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

pheno_table.txt{:bash}

:file

table with all AMR phenotypes

pheno_table.tsv

pointfinder_kma{:bash}

meta{:bash}

:map

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

pointfinder_kma{:bash}

:directory

directory holding kma results

pointfinder_kma

pointfinder_prediction{:bash}

meta{:bash}

:map

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

PointFinder_prediction.txt{:bash}

: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{:bash}

meta{:bash}

:map

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

PointFinder_results.txt{:bash}

:file

tab separated table with predicted point mutations leading to antibiotic resistance

PointFinder_results.txt

pointfinder_table{:bash}

meta{:bash}

:map

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

PointFinder_table.txt{:bash}

:file

predicted point mutations grouped into genes to which they belong

PointFinder_table.txt

resfinder_hit_in_genome_seq{:bash}

meta{:bash}

:map

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

ResFinder_Hit_in_genome_seq.fsa{:bash}

:file

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

ResFinder_Hit_in_genome_seq.fsa

resfinder_blast{:bash}

meta{:bash}

:map

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

resfinder_blast{:bash}

:directory

directory holding blast results

resfinder_kma

resfinder_kma{:bash}

meta{:bash}

:map

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

resfinder_kma{:bash}

:directory

directory holding kma results

resfinder_kma

resfinder_resistance_gene_seq{:bash}

meta{:bash}

:map

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

ResFinder_Resistance_gene_seq.fsa{:bash}

:file

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

ResFinder_Resistance_gene_seq.fsa

resfinder_results_table{:bash}

meta{:bash}

:map

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

ResFinder_results_table.txt{:bash}

:file

predicted resistance genes grouped by antibiotic class

ResFinder_results_table.txt

resfinder_results_tab{:bash}

meta{:bash}

:map

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

ResFinder_results_tab.txt{:bash}

:file

tab separated table with predicted resistance genes

ResFinder_results_tab.txt

resfinder_results{:bash}

meta{:bash}

:map

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

ResFinder_results.txt{:bash}

:file

predicted resistance genes grouped by antibiotic class and hit alignments to reference resistance genes

ResFinder_results.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainer
Github user marrip
get in touch
Ask a question on Slack Open an issue on GitHub