Snakemake

Changed

- --touch ignores missing files
- Fixed handling of local URIs with the wrapper directive.

Added

- Param functions can now also refer to threads. Changed
- Improved tutorial and docs.
- Made conda integration more robust.
- None is converted to NULL in R scripts.

Changed

- Improved config file handling and merging.
- Output files can be referred in params functions (i.e. lambda
wildcards, output: ...)
- Improved conda-environment creation.
- Jobs are cached, leading to reduced memory footprint.
- Fixed subworkflow handling in input functions.

Added

- Workflows can now be archived to a tarball with
`snakemake --archive my-workflow.tar.gz`. The archive contains all
input files, source code versioned with git and all software
packages that are defined via conda environments. Hence, the archive
allows to fully reproduce a workflow on a different machine. Such an
archive can be uploaded to Zenodo, such that your workflow is
secured in a self-contained, executable way for the future.
Changed
- Improved logging.
- Reduced memory footprint.
- Added a flag to automatically unpack the output of input functions.
- Improved handling of HTTP redirects with remote files.
- Improved exception handling with DRMAA.
- Scripts referred by the script directive can now use locally defined
external python modules.

Added

- Jobs can be restarted upon failure (--restart-times). Changed
- The docs have been restructured and improved. Now available under
snakemake.readthedocs.org.
- Changes in scripts show up with --list-code-changes.
- Duplicate output files now cause an error.
- Various bug fixes.

Added

- Ability to define isolated conda software environments (YAML) per
rule. Environments will be deployed by Snakemake upon workflow
execution.
- Command line argument --wrapper-prefix in order to overwrite the
default URL for looking up wrapper scripts. Changed
- --summary now displays the log files corresponding to each output
file.
- Fixed hangups when using run directive and a large number of jobs
- Fixed pickling errors with anonymous rules and run directive.
- Various small bug fixes