modules/mykrobe_predict

AMR predictions for supported species

fastqbamantimicrobial resistance

https://github.com/nf-core/modules/[...]/modules/nf-core/mykrobe/predict

Description

AMR predictions for supported species

Input

name:type

description

pattern

`meta`
`:map`

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

`seqs`
`:file`

BAM or FASTQ file

*.{bam,fastq.gz,fq.gz}

`species`
`:string`

Species to make AMR prediction against

*

Output

name:type

description

pattern

`csv`

`meta`
`:map`

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

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

AMR predictions in CSV format

*.csv

`json`

`meta`
`:map`

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

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

AMR predictions in JSON format

*.json

`versions_mykrobe`

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

The name of the process

`mykrobe`
`:string`

The name of the tool

`mykrobe --version 2>&1 | sed 's/^.*mykrobe v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`mykrobe`
`:string`

The name of the tool

`mykrobe --version 2>&1 | sed 's/^.*mykrobe v//'`
`:eval`

The expression to obtain the version of the tool

Tools

mykrobe
MIT

Antibiotic resistance prediction in minutes

http://www.mykrobe.com github.com/Mykrobe-tools/mykrobe/wiki https://github.com/Mykrobe-tools/mykrobe 10.1038/ncomms10063

modules/mykrobe_predict

Description

Input

`meta`
`:map`

`seqs`
`:file`

`species`
`:string`

Output

`csv`

`meta`
`:map`

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

`json`

`meta`
`:map`

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

`versions_mykrobe`

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

`mykrobe`
`:string`

`mykrobe --version 2>&1 | sed 's/^.*mykrobe v//'`
`:eval`

Topics

`versions`

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

`mykrobe`
`:string`

`mykrobe --version 2>&1 | sed 's/^.*mykrobe v//'`
`:eval`

Tools

mykrobe
MIT

maintainer

get in touch

modules/mykrobe_predict

Description

Input

meta :map

seqs :file

species :string

Output

csv

meta :map

${prefix}.csv :file

json

meta :map

${prefix}.json :file

versions_mykrobe

${task.process} :string

mykrobe :string

mykrobe --version 2>&1 | sed 's/^.*mykrobe v//' :eval

Topics

versions

${task.process} :string

mykrobe :string

mykrobe --version 2>&1 | sed 's/^.*mykrobe v//' :eval

Tools

mykrobeMIT

maintainer

get in touch

`meta`
`:map`

`seqs`
`:file`

`species`
`:string`

`csv`

`meta`
`:map`

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

`json`

`meta`
`:map`

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

`versions_mykrobe`

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

`mykrobe`
`:string`

`mykrobe --version 2>&1 | sed 's/^.*mykrobe v//'`
`:eval`

`versions`

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

`mykrobe`
`:string`

`mykrobe --version 2>&1 | sed 's/^.*mykrobe v//'`
`:eval`

mykrobe
MIT