modules/sratools_fasterqdump

Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).

sequencingFASTQdump

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

Description

Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).

Input

name:type

description

pattern

`meta`
`:map`

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

`sra`
`:directory`

Directory containing ETL data for the given SRA.

*/*.sra

`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

`reads`

`meta`
`:map`

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

`*.fastq.gz`
`:file`

Extracted FASTQ file or files if the sequencing reads are paired-end.

*.fastq.gz

`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_pigz`

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

The name of the process

`pigz`
`:string`

The name of the tool

`pigz --version 2>&1 | sed 's/pigz //g'`
`: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

`pigz`
`:string`

The name of the tool

`pigz --version 2>&1 | sed 's/pigz //g'`
`: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_fasterqdump

Description

Input

`meta`
`:map`

`sra`
`:directory`

`ncbi_settings`
`:file`

`certificate`
`:file`

Output

`reads`

`meta`
`:map`

`*.fastq.gz`
`:file`

`versions_sratools`

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

`sratools`
`:string`

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

`versions_pigz`

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

`pigz`
`:string`

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

Topics

`versions`

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

`sratools`
`:string`

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

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

`pigz`
`:string`

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

Tools

sratools
Public Domain

included in

maintainers

get in touch

modules/sratools_fasterqdump

Description

Input

meta:map

sra:directory

ncbi_settings:file

certificate:file

Output

reads

meta:map

*.fastq.gz:file

versions_sratools

${task.process}:string

sratools:string

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

versions_pigz

${task.process}:string

pigz:string

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

Topics

versions

${task.process}:string

sratools:string

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

${task.process}:string

pigz:string

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

Tools

sratools Public Domain

included in

maintainers

get in touch

`meta`
`:map`

`sra`
`:directory`

`ncbi_settings`
`:file`

`certificate`
`:file`

`reads`

`meta`
`:map`

`*.fastq.gz`
`:file`

`versions_sratools`

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

`sratools`
`:string`

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

`versions_pigz`

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

`pigz`
`:string`

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

`versions`

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

`sratools`
`:string`

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

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

`pigz`
`:string`

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

sratools
Public Domain