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
: 1memory
: 1GBcontainer
: flowcraft/sra-toolsversion
: 2.9.1-1