Unescaped quotes in generated bash shell script #3297
Description
Snakemake version
8.27.1
Describe the bug
When using the shell directive (bash script) with the config directive, associative arrays are added to a generated shell script. If a string in the config YAML file contains ' then the generated associative arrays contain unescaped double-quotes which causes a syntax error.
Logs
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 20
Rules claiming more threads will be scaled down.
Job stats:
job count
----- -------
test 1
total 1
Select jobs to execute...
Execute 1 jobs...
[Mon Feb 17 11:09:53 2025]
localrule test:
output: test.txt
jobid: 0
reason: Forced execution
resources: tmpdir=/tmp
/home/rosewood/Desktop/snakemake_shell/.snakemake/scripts/tmpz6rzz406.script.sh: line 9: unexpected EOF while looking for matching `''
/home/rosewood/Desktop/snakemake_shell/.snakemake/scripts/tmpz6rzz406.script.sh: line 13: syntax error: unexpected end of file
Not cleaning up /home/rosewood/Desktop/snakemake_shell/.snakemake/scripts/tmpz6rzz406.script.sh
RuleException:
CalledProcessError in file /home/rosewood/Desktop/snakemake_shell/Snakefile, line 9:
Command 'set -euo pipefail; bash /home/rosewood/Desktop/snakemake_shell/.snakemake/scripts/tmpz6rzz406.script.sh' returned non-zero exit status 1.
[Mon Feb 17 11:09:53 2025]
Error in rule test:
jobid: 0
output: test.txt
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-02-17T110953.594439.snakemake.log
WorkflowError:
At least one job did not complete successfully.
Minimal example
Snakefile
configfile: 'config.yaml'
rule test:
output:
'test.txt'
params:
d={'a': "foo'"}
script:
"script.sh"script.sh
#!/usr/bin/env bash
echo "hello" > "${snakemake_output[0]}"config.yaml
foo:
bar: "let's go"Run command snakemake test.txt --skip-script-cleanup -f
Additional context
Here is the generated bash script:
#!/usr/bin/env bash
declare -A snakemake_input=( )
declare -A snakemake_output=( [0]="test.txt" )
declare -A snakemake_params=( [0]="a" [d]="a" )
declare -A snakemake_wildcards=( )
declare -A snakemake_resources=( [0]="1" [_cores]="1" [1]="1" [_nodes]="1" [2]="/tmp" [tmpdir]="/tmp" )
declare -A snakemake_log=( )
declare -A snakemake_config=( [foo]="{'bar': "let's go"}" )
declare -A snakemake=( [_params_types]="{}" [threads]="1" [rule]="test" [bench_iteration]="None" [scriptdir]="/home/rosewood/Desktop/snakemake_shell" )
echo "hello" > "${snakemake_output[0]}"Culprit is declare -A snakemake_config=( [foo]="{'bar': "let's go"}" ). Note that the snakemake_params is also incorrect.
Potential patch
I've tried the following fix, which solves the above MWE but may incorrectly escape double quotes.
diff --git a/snakemake/script/__init__.py b/snakemake/script/__init__.py
index c802bc15..4a70c41b 100644
--- a/snakemake/script/__init__.py
+++ b/snakemake/script/__init__.py
@@ -468,7 +468,8 @@ class BashEncoder:
"""Converts a dictionary to an associative array"""
s = "( "
for k, v in d.items():
- s += f'[{k}]="{v}" '
+ formatted_v = f"{v}".replace('"', '\\"')
+ s += f'[{k}]="{formatted_v}" '
s += ")"
return s