Snakemake

Added

- onstart handler, that allows to add code that shall be only executed
before the actual workflow execution (not on dryrun).
- Parameters defined in the cluster config file are now accessible in
the job properties under the key "cluster".
- The wrapper directive can be considered stable. Changed
- Allow to use rule/job parameters with braces notation in cluster
config.
- Show a proper error message in case of recursion errors.
- Remove non-empty temp dirs.
- Don't set the process group of Snakemake in order to allow kill
signals from parent processes to be propagated.
- Fixed various corner case bugs.
- The params directive no longer converts a list `l` implicitly to
`" ".join(l)`.

Added

- New experimental wrapper directive, which allows to refer to
reusable [wrapper
scripts](https://bitbucket.org/snakemake/snakemake/wiki/Documentation#markdown-header-wrappers).
Wrappers are provided in the [Snakemake Wrapper
Repository](https://bitbucket.org/snakemake/snakemake-wrappers).
- David Koppstein implemented two new command line options to
constrain the execution of the DAG of job to sub-DAGs (--until and
--omit-from). Changed
- Fixed various bugs, e.g. with shadow jobs and --latency-wait.

Changed

- The params directive now fully supports non-string parameters.
Several bugs in the remote support were fixed.

Changed

- The missing remote module was added to the package.

Added

- Support for easy integration of external R and Python scripts via
the new [script
directive](https://bitbucket.org/snakemake/snakemake/wiki/Documentation#markdown-header-external-scripts).
- Chris Tomkins-Tinch has implemented support for remote files:
Snakemake can now handle input and output files from Amazon S3,
Google Storage, FTP, SFTP, HTTP and Dropbox.
- Simon Ye has implemented support for sandboxing jobs with [shadow
rules](https://bitbucket.org/snakemake/snakemake/wiki/Documentation#markdown-header-shadow-rules).

Changed

- Manuel Holtgrewe has fixed dynamic output files in combination with
multiple wildcards.
- It is now possible to add suffixes to all shell commands with
shell.suffix("mysuffix").
- Job execution has been refactored to spawn processes only when
necessary, resolving several problems in combination with huge
workflows consisting of thousands of jobs and reducing the memory
footprint.
- In order to reflect the new collaborative development model,
Snakemake has moved from my personal bitbucket account to
<http://snakemake.bitbucket.org>.

Changed

- Willem Ligtenberg has reduced the memory usage of Snakemake.
- Per Unneberg has improved config file handling to provide a more
intuitive overwrite behavior.
- Simon Ye has improved the test suite of Snakemake and helped with
setting up continuous integration via Codeship.
- The cluster implementation has been rewritten to use only a single
thread to wait for jobs. This avoids failures with large numbers of
jobs.
- Benchmarks are now writing tab-delimited text files instead of JSON.
- Snakemake now always requires to set the number of jobs with -j when
in cluster mode. Set this to a high value if your cluster does not
have restrictions.
- The Snakemake Conda package has been moved to the bioconda channel.
- The handling of Symlinks was improved, which made a switch to Python
3.3 as the minimum required Python version necessary.