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Indirect vs direct rule invocations raise different errors (when inputs use remote storage plugins)

bugSomething isn't workingSomething isn't working

Status: Open.

#3663 In snakemake/snakemake;

· jameshadfield opened on Jul 8, 2025

params doesn't correctly parse wildcards when using Path(workflow.basedir)

bugSomething isn't workingSomething isn't working

Status: Open.

#3654 In snakemake/snakemake;

· tbenavi1 opened on Jul 2, 2025

Shell command incorrectly shows as None for dryrun when using run directive in snakemake rule

bugSomething isn't workingSomething isn't working

Status: Open.

#3653 In snakemake/snakemake;

· tbenavi1 opened on Jul 2, 2025

Cannot enforce the config values passed through command line as string

bugSomething isn't workingSomething isn't working

Status: Open.

#3650 In snakemake/snakemake;

· TNalpat opened on Jun 30, 2025

Add <code>snakemake.utils.max_version</code> to avoid known regressions

enhancementNew feature or requestNew feature or request

Status: Open.

#3649 In snakemake/snakemake;

· mschilli87 opened on Jun 30, 2025

Regression: Config YAML validation with cross-file JSON Schema references fails in Snakemake &gt;= <code>9.6.0</code>

bugSomething isn't workingSomething isn't working

Status: Open.

#3648 In snakemake/snakemake;

· mschilli87 opened on Jun 30, 2025

Adding New Scheduler Plugin

questionFurther information is requestedFurther information is requested

Status: Open.

#3646 In snakemake/snakemake;

· AasishKumarSharma opened on Jun 24, 2025

Unexpected behaviour with wildcard_constraints and touch

bugSomething isn't workingSomething isn't working

Status: Open.

#3645 In snakemake/snakemake;

· jung-benjamin opened on Jun 24, 2025

Cyclic-ish dependencies

Status: Open.

#3644 In snakemake/snakemake;

· vadim0x60 opened on Jun 24, 2025

<code>profile</code> clashes with <code>--</code> argument separator

bugSomething isn't workingSomething isn't working

Status: Open.

#3642 In snakemake/snakemake;

· dariober opened on Jun 23, 2025

Cross-platform path handling: <code>str(Path)</code> breaks shell commands on Windows

enhancementNew feature or requestNew feature or request

Status: Open.

#3637 In snakemake/snakemake;

· lauraporta opened on Jun 20, 2025

Faster local executor in conda environments

enhancementNew feature or requestNew feature or request

Status: Open.

#3635 In snakemake/snakemake;

· tristan-f-r opened on Jun 17, 2025