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Migration between Snakemake versions

Snakemake is meant to remain backwards compatible as much as possible. However, sometimes, very rarely, we remove old almost unused features that have since then been replaced by new ones (so far, this happened only once, for Snakemake 8). Sometimes, new features are added that do not require, but make it strongly advisable to adapt workflows (e.g. because the new features provide a better user or recipient experience).

Below are migration hints for particular Snakemake versions.

Migrating to Snakemake 8

Workflow definitions

Snakemake 8 removes the support for four syntactical elements, which are all officially deprecated since multiple major releases:

  • Support for marking output files as dynamic has been removed. You should instead use checkpoints <snakefiles-checkpoints>.
  • Support for the version directive has been removed. You should use the conda <integrated_package_management> or container <apptainer> integration instead.
  • Support for the subworkflow directive has been removed. You should use the module directive <snakefiles-modules> instead, which provides the same functionality in a more general way.
  • Support for remote providers has been removed. You should use storage plugins <storage-support> instead. Most of the old remote providers have been migrated into the new storage plugins (see the Snakemake plugin catalog.). Two former remote providers have been migrated into Snakemake wrappers instead, namely the NCBI and ENA remote providers, which are now replaced by the entrez/efetch and the ena wrappers.

Command line interface

The command line interface of Snakemake 8 has a lot of new options which are best explored using:

snakemake --help

Morever, some options have been renamed:

  • All the execution backends have been moved into plugins. When you used e.g. --kubernetes and corresponding options before, you should now use --executor kubeternes and check the Snakemake plugin catalog for the new options. The same holds for all other execution backends, see here.
  • The --use-conda and --use-singularity options are deprecated. Instead you should now use --software-deployment-method conda or --software-deployment-method apptainer or --software-deployment-method conda apptainer if you need both.

Profiles

Profiles can now be versioned. If your profile makes use of settings that are available in version 8 or later, use the filename config.v8+.yaml for the profile configuration (see profiles).

API

The Snakemake API has been completely rewritten into a modern dataclass based approach. The traditional central snakemake() function is gone. For an example how to use the new API, check out the Snakemake CLI implementation here.