reference.snake

# 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}
    """