Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

sra{:bash}

:directory

Directory containing ETL data for the given SRA.

*/*.sra

ncbi_settings{:bash}

:file

An NCBI user settings file.

*.mkfg

certificate{:bash}

: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{:bash}

meta{:bash}

:map

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

*.fastq.gz{:bash}

:file

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

*.fastq.gz

versions_sratools{:bash}

${task.process}{:bash}

:string

The name of the process

sratools{:bash}

:string

The name of the tool

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

:eval

The expression to obtain the version of the tool

versions_pigz{:bash}

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed 's/pigz //g'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

sratools{:bash}

:string

The name of the tool

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

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed 's/pigz //g'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
fetchngspathogensurveillance
maintainers
Github user Midnighter
Github user gallvp
get in touch
Ask a question on Slack Open an issue on GitHub