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{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
fetchngspathogensurveillance
maintainers
Github user Midnighter
Github user gallvp
get in touch
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