modules/hamronization_summarize

Tool to summarize and combine all hAMRonization reports into a single file

amrantimicrobial resistancereporting

https://github.com/nf-core/modules/[...]/modules/nf-core/hamronization/summarize

Description

Tool to summarize and combine all hAMRonization reports into a single file

Input

name:type

description

pattern

`reports`
`:file`

List of multiple hAMRonization reports in either JSON or TSV format

*.{json,tsv}

`format`
`:string`

Type of final combined report file to be produced

tsv|json|interactive

Output

name:type

description

pattern

`json`

`hamronization_combined_report.json`
`:file`

hAMRonised summary in JSON format

*.json

`tsv`

`hamronization_combined_report.tsv`
`:file`

hAMRonised summary in TSV format

*.json

`html`

`hamronization_combined_report.html`
`:file`

hAMRonised summary in HTML format

*.html

`versions_hamronization`

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

The name of the process

`hamronization`
`:string`

The name of the tool

`hamronize --version 2>&1 | sed 's/hamronize //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`hamronization`
`:string`

The name of the tool

`hamronize --version 2>&1 | sed 's/hamronize //'`
`:eval`

The expression to obtain the version of the tool

Tools

hamronization
GNU Lesser General Public v3 (LGPL v3)

Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification

github.com/pha4ge/hAMRonization https://github.com/pha4ge/hAMRonization

modules/hamronization_summarize

Description

Input

`reports`
`:file`

`format`
`:string`

Output

`json`

`hamronization_combined_report.json`
`:file`

`tsv`

`hamronization_combined_report.tsv`
`:file`

`html`

`hamronization_combined_report.html`
`:file`

`versions_hamronization`

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

`hamronization`
`:string`

`hamronize --version 2>&1 | sed 's/hamronize //'`
`:eval`

Topics

`versions`

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

`hamronization`
`:string`

`hamronize --version 2>&1 | sed 's/hamronize //'`
`:eval`

Tools

hamronization
GNU Lesser General Public v3 (LGPL v3)

included in

maintainer

get in touch

modules/hamronization_summarize

Description

Input

reports :file

format :string

Output

json

hamronization_combined_report.json :file

tsv

hamronization_combined_report.tsv :file

html

hamronization_combined_report.html :file

versions_hamronization

${task.process} :string

hamronization :string

hamronize --version 2>&1 | sed 's/hamronize //' :eval

Topics

versions

${task.process} :string

hamronization :string

hamronize --version 2>&1 | sed 's/hamronize //' :eval

Tools

hamronizationGNU Lesser General Public v3 (LGPL v3)

included in

maintainer

get in touch

`reports`
`:file`

`format`
`:string`

`json`

`hamronization_combined_report.json`
`:file`

`tsv`

`hamronization_combined_report.tsv`
`:file`

`html`

`hamronization_combined_report.html`
`:file`

`versions_hamronization`

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

`hamronization`
`:string`

`hamronize --version 2>&1 | sed 's/hamronize //'`
`:eval`

`versions`

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

`hamronization`
`:string`

`hamronize --version 2>&1 | sed 's/hamronize //'`
`:eval`

hamronization
GNU Lesser General Public v3 (LGPL v3)