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# vim: syntax=python tabstop=4 expandtab
# coding: utf-8
'''
@author: jpreuss
Provides rules for reference related modifications
'''
from snakemake.remote.FTP import RemoteProvider as FTPRemoteProvider
FTP = FTPRemoteProvider()
rule genome_download:
input:
FTP.remote(expand(config['reference']['genome_URL'], **config['reference']), keep_local = True)
output:
GENOME
threads: 1
message:
'Downloading gencode genome reference.'
shell:
"""
zcat -f {input} > {output}
"""
rule annotation_download:
input:
FTP.remote(expand(config['reference']['annotation_URL'], **config['reference']), keep_local = True)
output:
ANNOTATION
threads: 1
message:
'Downloading gencode annotation reference.'
shell:
"""
zcat -f {input} > {output}
"""