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from snakemake.utils import min_version
from snakemake import __version__
print(__version__, file=sys.stderr)
shell.prefix("source ~/.bashrc; ")
#min_version("2.1")
TEST = "abc"
onstart:
print("Workflow starting")
print("Log:")
print(log)
onsuccess:
print("Workflow finished")
print("Log:")
print(log)
onerror:
print("Workflow failed")
print("Log:")
print(log)
ruleorder: rule2 > rule4
def testin(wildcards):
return "test.in"
def version():
return "3.3"
rule rule1:
# This rule creates an intermediate file.
input:
'test.inter'
output: 'dir/test.out'
log: a='log/logfile.log'
version: version()
threads: 3
shell:
'if [ {threads} -ne 3 ]; then echo "This test has to be run with -j3 in order to succeed!"; exit 1; fi; ' \
'echo {TEST}; echo {version}; cp {input[0]} {output[0]}; ' # append a comment
'echo test > {log.a}'
rule rule2:
input: testin
output: 'test.inter'
message: 'Copying {input[0]} to {output[0]}'
shell:
'''
cp {input[0]} {output[0]}
'''
rule rule4:
input: "test.in"
output: "test.inter"
shell: "cp {input} {output}"
# this should be ignored since test.in is present
rule rule3:
input: "dir/{a}.out"
output: "{a}.in"
shell: "cp {input} {output}"
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