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Notebooks paths are made absolute and cannot be linked to upstream rules anymore

bugSomething isn't workingSomething isn't working

Status: Open.

#4236 In snakemake/snakemake;

· raffienficiaud opened on Jun 22, 2026

--print-compilation ignores SyntaxErrors

bugSomething isn't workingSomething isn't working

Status: Open.

#4235 In snakemake/snakemake;

· schnea opened on Jun 19, 2026

Unexpected interaction between local() inputs, Slurm execution, and FS staging

bugSomething isn't workingSomething isn't working

Status: Open.

#4233 In snakemake/snakemake;

· jmzhang1911 opened on Jun 18, 2026

Unable to obtain modification time of a dropped file (datalad/git-annex)

bugSomething isn't workingSomething isn't working

Status: Open.

#4229 In snakemake/snakemake;

· just-meng opened on Jun 13, 2026

how to launch containerized snakemake that submits jobscripts using the same container

Status: Open.

#4226 In snakemake/snakemake;

· rsdmse opened on Jun 10, 2026

fix for benchmark when rule using run clause reports no stats

bugSomething isn't workingSomething isn't working

Status: Open.

#4224 In snakemake/snakemake;

· john-granieri opened on Jun 10, 2026

perf: snakemake dry-run spends most wall-clock on conda verification and eager module imports

Status: Open.

Task

#4220 In snakemake/snakemake;

· Hocnonsense opened on Jun 6, 2026

Remote scripts do not trigger job re-execution when updated

bugSomething isn't workingSomething isn't working

Status: Open.

#4217 In snakemake/snakemake;

· Naisha-Gajkandh opened on Jun 4, 2026

Regression after PR #4079: TypeError: Object of type PosixPath is not JSON serializable

bugSomething isn't workingSomething isn't working

Status: Open.

#4215 In snakemake/snakemake;

· mmmaat opened on Jun 3, 2026

Race condition in output_mintime with temp inputs may give an error

bugSomething isn't workingSomething isn't working

Status: Open.

#4213 In snakemake/snakemake;

· limwz01 opened on Jun 2, 2026

Dry-run crashes with KeyError when a checkpoint-driven grouped job is present

Status: Open.

#4202 In snakemake/snakemake;

· alessandrogentili001 opened on May 25, 2026

Question about modular design

bugSomething isn't workingSomething isn't working

Status: Open.

#4201 In snakemake/snakemake;

· jmzhang1911 opened on May 23, 2026