try:
from generator.process import Process
except ImportError:
from assemblerflow.generator.process import Process
[docs]class DownloadReads(Process):
"""Process template interface for reads downloading from SRA and NCBI
This process is set with:
- ``input_type``: accessions
- ``output_type`` fastq
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
self.input_type = "accessions"
self.output_type = "fastq"
self.params = {
"asperaKey": {
"default": "null",
"description":
"Downloads fastq accessions from ENA using Aspera Connect "
"by providing the private-key file "
"'asperaweb_id_dsa.openssh' normally found in "
"~/.aspera/connect/etc/asperaweb_id_dsa.openssh "
"(Default: null)"
}
}
self.directives = {"reads_download": {
"cpus": 1,
"memory": "'1GB'",
"container": "ummidock/getseqena",
"version": "0.4.0-2"
}}