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 type:
accessions
- Output type:
fastq
Note
The default input parameter for Accessions data is --accessions
.
- 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.
reads/<accession>
: Stores the reads for each provided accession.
None.
cpus
: 1memory
: 1GBcontainer
: flowcraft/sra-toolsversion
: 2.9.1-1