modules/geofetch

geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA

GEOexpressionmicroarraysequencing

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

Description

geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA

Input

name:type

description

pattern

`geo_accession`
`:string`

GEO accession ID

Output

name:type

description

pattern

`samples`

`${geo_accession}`
`:file`

List of sample files fetched

${geo_accession}/*.CEL.gz

`${geo_accession}/*.CEL.gz`
`:file`

List of sample files fetched

${geo_accession}/*.CEL.gz

`versions_geofetch`

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

The process the versions were collected from

`geofetch`
`:string`

The tool name

`geofetch --version 2>&1 | sed '1!d; s/^geofetch //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`geofetch`
`:string`

The tool name

`geofetch --version 2>&1 | sed '1!d; s/^geofetch //'`
`:eval`

The expression to obtain the version of the tool

Tools

geofetch
BSD-2-clause

Downloads data and metadata from GEO and SRA and creates standard PEPs.

args_id: $args

http://geofetch.databio.org https://github.com/pepkit/geofetch

modules/geofetch

Description

Input

`geo_accession`
`:string`

Output

`samples`

`${geo_accession}`
`:file`

`${geo_accession}/*.CEL.gz`
`:file`

`versions_geofetch`

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

`geofetch`
`:string`

`geofetch --version 2>&1 | sed '1!d; s/^geofetch //'`
`:eval`

Topics

`versions`

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

`geofetch`
`:string`

`geofetch --version 2>&1 | sed '1!d; s/^geofetch //'`
`:eval`

Tools

geofetch
BSD-2-clause

maintainer

get in touch

modules/geofetch

Description

Input

geo_accession:string

Output

samples

${geo_accession}:file

${geo_accession}/*.CEL.gz:file

versions_geofetch

${task.process}:string

geofetch:string

geofetch --version 2>&1 | sed '1!d; s/^geofetch //':eval

Topics

versions

${task.process}:string

geofetch:string

geofetch --version 2>&1 | sed '1!d; s/^geofetch //':eval

Tools

geofetch BSD-2-clause

maintainer

get in touch

`geo_accession`
`:string`

`samples`

`${geo_accession}`
`:file`

`${geo_accession}/*.CEL.gz`
`:file`

`versions_geofetch`

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

`geofetch`
`:string`

`geofetch --version 2>&1 | sed '1!d; s/^geofetch //'`
`:eval`

`versions`

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

`geofetch`
`:string`

`geofetch --version 2>&1 | sed '1!d; s/^geofetch //'`
`:eval`

geofetch
BSD-2-clause