fix: correctly set params in bash scripts (#3188)

This PR tweaks the Bash script test to trigger the bug raised in #3187 ### QC  * [x] The PR contains a test case for the changes or the changes are already covered by an existing test case. * [ ] The documentation (`docs/`) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).  ## Summary by CodeRabbit - **Tests** - Enhanced error handling in the script with improved shell options. - Added a conditional test to validate parameters before executing existing commands. - Updated input parameter in the `bash` rule for clarity without affecting functionality. - **New Features** - Improved parameter handling in the Bash script generation process for enhanced functionality.  --------- Co-authored-by: coderabbitai[bot] <136622811 coderabbitai[bot]@users.noreply.github.com>
snakemake · Nov 11, 2024 · 07ddab5 · 07ddab5
1 parent 5f651d2
commit 07ddab5
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/snakemake/script/__init__.py b/snakemake/script/__init__.py
@@ -419,7  419,8 @@ def encode_snakemake(self, smk: Snakemake) -> str:
         for var in vars(smk):
             val = getattr(smk, var)
             if var in self.namedlists:
-                aa = f"{self.prefix}_{var.strip('_').lower()}={self.encode_namedlist(val)}"
                 suffix = "params" if var == "_params_store" else var.strip("_").lower()
                 aa = f"{self.prefix}_{suffix}={self.encode_namedlist(val)}"
                 arrays.append(aa)
             elif var in self.dicts:
                 aa = f"{self.prefix}_{var.strip('_').lower()}={self.dict_to_aa(val)}"
@@ -1438,7  1439,14 @@ def generate_preamble(
             scriptdir=path.get_basedir().get_path_or_uri(),
         )
 
-        namedlists = ["input", "output", "log", "resources", "wildcards", "params"]
         namedlists = [
             "input",
             "output",
             "log",
             "resources",
             "wildcards",
             "_params_store",
         ]
         dicts = ["config"]
         encoder = BashEncoder(namedlists=namedlists, dicts=dicts)
         preamble = encoder.encode_snakemake(snakemake)

diff --git a/tests/test_script/Snakefile b/tests/test_script/Snakefile
@@ -104,7  104,7 @@ rule:
 rule bash:
     input:
         "test2.in",
-        named_input="test.in",
         named="test.in",
     output:
         "bash.out"
     params:

diff --git a/tests/test_script/scripts/test.sh b/tests/test_script/scripts/test.sh
@@ -1,4  1,7 @@
 #!/usr/bin/env bash
 set -euo pipefail
 exec 2> "${snakemake_log[0]}"
 test "${snakemake_params[string]}" = "foo"
 
 echo "The first input file is ${snakemake_input[0]}" > "${snakemake_output[0]}" 2> "${snakemake_log[0]}"
 echo "The named input file is ${snakemake_input[named]}" >> "${snakemake_output[0]}" 2>> "${snakemake_log[0]}"