modules/sratools_prefetch

Download sequencing data from the NCBI Sequence Read Archive (SRA).

sequencingfastqprefetch

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

Description

Download sequencing data from the NCBI Sequence Read Archive (SRA).

Input

name:type

description

pattern

`meta`
`:map`

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

`id`
`:string`

A string denoting an SRA id.

`ncbi_settings`
`:file`

An NCBI user settings file.

*.mkfg

`certificate`
`:file`

Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit

*.cart

Output

name:type

description

pattern

`sra`

`meta`
`:map`

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

`${id}`
`:directory`

Directory containing SRA data files

*/*.sra

`versions_sratools`

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

The name of the process

`sratools`
`:string`

The name of the tool

`prefetch --version 2>&1 | grep -Eo '[0-9.]+'`
`:eval`

The expression to obtain the version of the tool

`versions_curl`

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

The name of the process

`curl`
`:string`

The name of the tool

`curl --version | sed '1!d;s/^curl //; s/ .*//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`sratools`
`:string`

The name of the tool

`prefetch --version 2>&1 | grep -Eo '[0-9.]+'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`curl`
`:string`

The name of the tool

`curl --version | sed '1!d;s/^curl //; s/ .*//'`
`:eval`

The expression to obtain the version of the tool

Tools

sratools
Public Domain

SRA Toolkit and SDK from NCBI

github.com/ncbi/sra-tools github.com/ncbi/sra-tools/wiki https://github.com/ncbi/sra-tools

modules/sratools_prefetch

Description

Input

`meta`
`:map`

`id`
`:string`

`ncbi_settings`
`:file`

`certificate`
`:file`

Output

`sra`

`meta`
`:map`

`${id}`
`:directory`

`versions_sratools`

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

`sratools`
`:string`

`prefetch --version 2>&1 | grep -Eo '[0-9.]+'`
`:eval`

`versions_curl`

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

`curl`
`:string`

`curl --version | sed '1!d;s/^curl //; s/ .*//'`
`:eval`

Topics

`versions`

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

`sratools`
`:string`

`prefetch --version 2>&1 | grep -Eo '[0-9.]+'`
`:eval`

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

`curl`
`:string`

`curl --version | sed '1!d;s/^curl //; s/ .*//'`
`:eval`

Tools

sratools
Public Domain

included in

maintainers

get in touch

modules/sratools_prefetch

Description

Input

meta:map

id:string

ncbi_settings:file

certificate:file

Output

sra

meta:map

${id}:directory

versions_sratools

${task.process}:string

sratools:string

prefetch --version 2>&1 | grep -Eo '[0-9.]+':eval

versions_curl

${task.process}:string

curl:string

curl --version | sed '1!d;s/^curl //; s/ .*//':eval

Topics

versions

${task.process}:string

sratools:string

prefetch --version 2>&1 | grep -Eo '[0-9.]+':eval

${task.process}:string

curl:string

curl --version | sed '1!d;s/^curl //; s/ .*//':eval

Tools

sratools Public Domain

included in

maintainers

get in touch

`meta`
`:map`

`id`
`:string`

`ncbi_settings`
`:file`

`certificate`
`:file`

`sra`

`meta`
`:map`

`${id}`
`:directory`

`versions_sratools`

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

`sratools`
`:string`

`prefetch --version 2>&1 | grep -Eo '[0-9.]+'`
`:eval`

`versions_curl`

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

`curl`
`:string`

`curl --version | sed '1!d;s/^curl //; s/ .*//'`
`:eval`

`versions`

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

`sratools`
`:string`

`prefetch --version 2>&1 | grep -Eo '[0-9.]+'`
`:eval`

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

`curl`
`:string`

`curl --version | sed '1!d;s/^curl //; s/ .*//'`
`:eval`

sratools
Public Domain