modules/rgi_main

Predict antibiotic resistance from protein or nucleotide data

bacteriafastaantibiotic resistance

https://github.com/nf-core/modules/[...]/modules/nf-core/rgi/main

Description

Predict antibiotic resistance from protein or nucleotide data

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

Nucleotide or protein sequences in FASTA format

*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}

`card`
`:directory`

Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).

*/

`wildcard`
`:directory`

Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions).

*/

Output

name:type

description

pattern

`json`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.json`
`:file`

JSON formatted file with RGI results

${prefix}.{json}

`tsv`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}.txt`
`:file`

Tab-delimited file with RGI results

${prefix}.txt

`tmp`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`temp/`
`:directory`

Directory containing various intermediate files

temp/

`tool_version`

`RGI_VERSION`
`:string`

The version of the tool in string format (useful for downstream tools such as hAMRronization)

`db_version`

`DB_VERSION`
`:string`

The version of the used database in string format (useful for downstream tools such as hAMRronization)

`versions_rgi`

`${task.process}`
`:string`

The name of the process

`rgi`
`:string`

The name of the tool

`rgi main --version`
`:eval`

The expression to obtain the version of the tool

`versions_db`

`${task.process}`
`:string`

The name of the process

`rgi-database`
`:string`

The name of the tool

`echo \$DB_VERSION`
`:eval`

The expression to obtain the version of the tool

`versions_kma`

`${task.process}`
`:string`

The name of the process

`kma`
`:string`

The name of the tool

`kma -v | sed 's/KMA-//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`rgi`
`:string`

The name of the tool

`rgi main --version`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`rgi-database`
`:string`

The name of the tool

`echo \$DB_VERSION`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`kma`
`:string`

The name of the tool

`kma -v | sed 's/KMA-//'`
`:eval`

The expression to obtain the version of the tool

Tools

rgi
https://card.mcmaster.ca/about

This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website

card.mcmaster.ca github.com/arpcard/rgi 10.1093/nar/gkz935

modules/rgi_main

Description

Input

meta :map

fasta :file

card :directory

wildcard :directory

Output

json

meta :map

${prefix}.json :file

tsv

meta :map

${prefix}.txt :file

tmp

meta :map

temp/ :directory

tool_version

RGI_VERSION :string

db_version

DB_VERSION :string

versions_rgi

${task.process} :string

rgi :string

rgi main --version :eval

versions_db

${task.process} :string

rgi-database :string

echo \$DB_VERSION :eval

versions_kma

${task.process} :string

kma :string

kma -v | sed 's/KMA-//' :eval

Topics

versions

${task.process} :string

rgi :string

rgi main --version :eval

${task.process} :string

rgi-database :string

echo \$DB_VERSION :eval

${task.process} :string

kma :string

kma -v | sed 's/KMA-//' :eval

Tools

rgihttps://card.mcmaster.ca/about

included in

maintainers

get in touch

`meta`
`:map`

`fasta`
`:file`

`card`
`:directory`

`wildcard`
`:directory`

`json`

`meta`
`:map`

`${prefix}.json`
`:file`

`tsv`

`meta`
`:map`

`${prefix}.txt`
`:file`

`tmp`

`meta`
`:map`

`temp/`
`:directory`

`tool_version`

`RGI_VERSION`
`:string`

`db_version`

`DB_VERSION`
`:string`

`versions_rgi`

`${task.process}`
`:string`

`rgi`
`:string`

`rgi main --version`
`:eval`

`versions_db`

`${task.process}`
`:string`

`rgi-database`
`:string`

`echo \$DB_VERSION`
`:eval`

`versions_kma`

`${task.process}`
`:string`

`kma`
`:string`

`kma -v | sed 's/KMA-//'`
`:eval`

`versions`

`${task.process}`
`:string`

`rgi`
`:string`

`rgi main --version`
`:eval`

`${task.process}`
`:string`

`rgi-database`
`:string`

`echo \$DB_VERSION`
`:eval`

`${task.process}`
`:string`

`kma`
`:string`

`kma -v | sed 's/KMA-//'`
`:eval`

rgi
https://card.mcmaster.ca/about