Smk Simple Slurm Versions Save

[!WARNING] This is the final release to support Snakemake versions 5, 6, and 7.

Example that specifies memory in GB instead of MB (mem-gb)

Example that shares a profile between pipelines, and includes the name of the Snakefile in the path to the logs (shared-logs) (Issue #12)

Update [job grouping][grouping] example to better allocate resources (requires minimum of Snakemake version 7.11.0) (Snakemake Issue #872)

Example that uses a job array to submit many jobs at once (job-array)

Example that uses --slurm (slurm-native, requires Snakemake 7.19.0+)

Example that logs stdout and stderr to separate files (separate-stderr) (Issue #14)

Example that conditionally specifies a resource for a subset of rules (TomHarrop, #16, #17)

Example that lists multiple partitions for Slurm to choose from (TomHarrop, #16, #17)

New status script status-sacct-robust.sh that re-runs sacct multiple times if it fails to return a valid status. This is more robust and is recommended if you notice Snakemake unexpectedly re-submits jobs that are still pending or running. See Issue #9 for discussion

Example with job grouping

Link to Christian's profile for AWS ParallelCluster

Example that uses pinned conda environments (pinned-conda-envs) (requires minimum of Snakemake version 7.8.0)

Example that inserts the current date in the log file paths (log-file-date)

Example rule with thousands of input files (many-input-files)

Full support for custom status scripts in a multi-cluster setup (requires minimum of Snakemake version 7.1.1)

Example with cluster-cancel (requires minimum of Snakemake version 7.0.0)

Reduce the default settings for max-jobs-per-second and max-status-checks-per-second to avoid stressing Slurm

Example of running rules in Singularity containers (CreRecombinase, #2)

Initial release