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target-DNAseq/src/reference.snake
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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} | |
""" |