Created
June 21, 2021 19:10
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Snakemake conditional execution example bug?
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# a target rule to define the desired final output | |
rule all: | |
input: | |
"aggregated/a.txt", | |
"aggregated/b.txt" | |
# the checkpoint that shall trigger re-evaluation of the DAG | |
checkpoint somestep: | |
input: | |
"samples/{sample}.txt" | |
output: | |
"somestep/{sample}.txt" | |
shell: | |
# simulate some output value | |
"echo {wildcards.sample} > somestep/{wildcards.sample}.txt" | |
# intermediate rule | |
rule intermediate: | |
input: | |
"somestep/{sample}.txt" | |
output: | |
"post/{sample}.txt" | |
shell: | |
"touch {output}" | |
# alternative intermediate rule | |
rule alt_intermediate: | |
input: | |
"somestep/{sample}.txt" | |
output: | |
"alt/{sample}.txt" | |
shell: | |
"touch {output}" | |
# input function for the rule aggregate | |
def aggregate_input(wildcards): | |
# decision based on content of output file | |
# Important: use the method open() of the returned file! | |
# This way, Snakemake is able to automatically download the file if it is generated in | |
# a cloud environment without a shared filesystem. | |
with checkpoints.somestep.get(sample=wildcards.sample).output[0].open() as f: | |
if f.read().strip() == "a": | |
return "post/{sample}.txt" | |
else: | |
return "alt/{sample}.txt" | |
rule aggregate: | |
input: | |
aggregate_input | |
output: | |
"aggregated/{sample}.txt" | |
shell: | |
"touch {output}" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# a target rule to define the desired final output | |
rule all: | |
input: | |
"aggregated/a.txt", | |
"aggregated/b.txt" | |
# the checkpoint that shall trigger re-evaluation of the DAG | |
checkpoint somestep: | |
output: | |
"somestep/{sample}.txt" | |
shell: | |
# simulate some output value | |
"echo {wildcards.sample} > somestep/{wildcards.sample}.txt" | |
# intermediate rule | |
rule intermediate: | |
input: | |
"somestep/{sample}.txt" | |
output: | |
"post/{sample}.txt" | |
shell: | |
"touch {output}" | |
# alternative intermediate rule | |
rule alt_intermediate: | |
input: | |
"somestep/{sample}.txt" | |
output: | |
"alt/{sample}.txt" | |
shell: | |
"touch {output}" | |
# input function for the rule aggregate | |
def aggregate_input(wildcards): | |
# decision based on content of output file | |
# Important: use the method open() of the returned file! | |
# This way, Snakemake is able to automatically download the file if it is generated in | |
# a cloud environment without a shared filesystem. | |
with checkpoints.somestep.get(sample=wildcards.sample).output[0].open() as f: | |
if f.read().strip() == "a": | |
return "post/{sample}.txt" | |
else: | |
return "alt/{sample}.txt" | |
rule aggregate: | |
input: | |
aggregate_input | |
output: | |
"aggregated/{sample}.txt" | |
shell: | |
"touch {output}" |
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