modules/rgi_cardannotation

Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data

bacteriafastaantibiotic resistance

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

Description

Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data

Input

name:type

description

pattern

`card`
`:directory`

Directory containing the CARD database

*/

Output

name:type

description

pattern

`db`

`card_database_processed`
`:directory`

Directory containing the processed CARD database files

*/

`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 module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI.

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

modules/rgi_cardannotation

Description

Input

`card`
`:directory`

Output

`db`

`card_database_processed`
`: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

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

included in

maintainers

get in touch

modules/rgi_cardannotation

Description

Input

card :directory

Output

db

card_database_processed :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

`card`
`:directory`

`db`

`card_database_processed`
`: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