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README.md

Examples

Each directory contains an example usage of the simple slurm profile. You can run them on your cluster to confirm the expected behavior.

  • cluster-cancel - Cancel all submitted jobs with scancel when the main Snakemake process is cancelled (requires Snakemake 7.0.0+)

  • conditional-resource - Conditionally specify a resource for a subset of rules

  • dynamic-resources - Increase memory for a rule on restart after each failed attempt

  • job-array - Use a Slurm job array to quickly execute a rule that must be run thousands of times

  • job-grouping - Adapt profile to allow job grouping

  • jobs-per-second - Measure how many jobs Snakemake can submit to Slurm per second

  • list-partitions - List multiple partitions for Slurm to choose from

  • log-file-date - Insert the current date into the log file path

  • many-input-files - Use a custom jobscript when a rule has many thousands of input files

  • mem-gb - Specify memory in GB

  • multi-cluster - Submit jobs to more than one cluster (requires Snakemake 7.1.1+)

  • out-of-memory - Trigger an out-of-memory error. Snakemake can handle this by default

  • pinned-conda-envs - Pin packages in conda environments

  • separate-stderr - Log stdout and stderr to separate files

  • shared-logs - Share the same profile config.yaml between multiple pipelines, but include the name of the Snakefile in the path to the log files

  • singularity - Run a rule inside a singularity container

  • slurm-native - Use Snakemake's native Slurm support (--slurm, requires Snakemake 7.19.0+)

  • threads - Increase the threads for a rule. It is responsive to --jobs. In other words, it will scale down the number of threads used if there aren't enough available (thus make sure to pass {threads} to the software you are running). This mainly applies when running the rules locally (i.e. without the profile). When submitting to the cluster, --jobs refers literally to jobs, not cores like in local mode

  • time-integer - Specify --time as an integer (minutes)

  • time-string - Specify the time as "days-hours:minutes:seconds"

  • timeout - Trigger a timeout error. Snakemake requires the assistance of a custom script to --cluster-status to handle this error. Otherwise it just stalls indefinitely