The profile has been updated to use the cluster submission features introduced in Snakemake 8+ (JoshLoecker, #21, #23)
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 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