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|
# a target rule to define the desired final output
rule all:
input:
"processed2.txt",
# the checkpoint that shall trigger re-evaluation of the DAG
# an number of file is created in a defined directory
checkpoint somestep:
output:
directory("my_directory/"),
shell:
"""
mkdir my_directory/
cd my_directory
for i in 1 2 3; do touch $i.txt; done
"""
# input function for rule aggregate, return paths to all files produced by the checkpoint 'somestep'
def aggregate_input(wildcards):
checkpoint_output = checkpoints.somestep.get(**wildcards).output[0]
return expand(
"my_directory/{i}.txt",
i=glob_wildcards(os.path.join(checkpoint_output, "{i}.txt")).i,
)
rule aggregate:
input:
aggregate_input,
output:
"aggregated.txt",
shell:
"echo AGGREGATED > {output}"
# Fail here if the job runs again, as we want to ensure that snakemake does not false trigger a rerun
# as reported in issue #1818.
rule process:
input:
"aggregated.txt",
output:
"processed.txt",
shell:
"exit 1; echo PROCESSED > {output}"
rule process2:
input:
"processed.txt",
output:
"processed2.txt",
shell:
"echo PROCESSED2 > {output}"
|
