SRA-TOOLS FASTERQ-DUMP¶
Download FASTQ files from SRA.
Example¶
This wrapper can be used in the following way:
rule get_fastq_pe:
output:
# the wildcard name must be accession, pointing to an SRA number
"data/{accession}_1.fastq",
"data/{accession}_2.fastq"
params:
# optional extra arguments
extra=""
threads: 6 # defaults to 6
wrapper:
"0.74.0/bio/sra-tools/fasterq-dump"
rule get_fastq_se:
output:
"data/{accession}.fastq"
params:
extra=""
threads: 6
wrapper:
"0.74.0/bio/sra-tools/fasterq-dump"
Note that input, output and log file paths can be chosen freely. When running with
snakemake --use-conda
the software dependencies will be automatically deployed into an isolated environment before execution.
Software dependencies¶
sra-tools>2.9.1
Authors¶
- Johannes Köster
- Derek Croote
Code¶
__author__ = "Johannes Köster, Derek Croote"
__copyright__ = "Copyright 2020, Johannes Köster"
__email__ = "johannes.koester@uni-due.de"
__license__ = "MIT"
import os
import tempfile
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
outdir = os.path.dirname(snakemake.output[0])
if outdir:
outdir = "--outdir {}".format(outdir)
extra = snakemake.params.get("extra", "")
with tempfile.TemporaryDirectory() as tmp:
shell(
"fasterq-dump --temp {tmp} --threads {snakemake.threads} "
"{extra} {outdir} {snakemake.wildcards.accession} {log}"
)