fasterq_dump

Purpose

This component downloads reads from the SRA public databases from a list of accessions. This component uses fasterq-dump from NCBI sra-tools. fasterq-dump increases the download speed in comparison from fastq-dump by multi-threading the extraction of FASTQ from SRA-accessions. The reads for each accession are then emitted through the main output of this component to any other component (or components) that receive FastQ data.

Input/Output type

  • Input type: accessions
  • Output type: fastq

Note

The default input parameter for Accessions data is --accessions.

Parameters

  • option_file: This options enables the option-file parameter of

fasterq-dump, allowing parameters to be passed. - compress_fastq: This options allows users to disable the compression of the fastq files resulting from this component. The default (true) behavior compresses the fastq files to fastq.gz.

Published results

  • reads/<accession>: Stores the reads for each provided accession.

Published reports

None.

Default directives

  • cpus: 1
  • memory: 1GB
  • container: flowcraft/sra-tools
  • version: 2.9.1-1