Snakemake

Changed

- Fix a followup bug in Namedlist where a single item was not returned
as string.

Changed

- The --wrapper-prefix flag now also affects where the corresponding
environment definition is fetched from.
- Fix bug where empty output file list was recognized as containing
duplicates (issue 574).

Changed

- Fix --conda-prefix to be passed to all jobs.
- Fix cleanup issue with scripts that fail to download.

Added

- An NCBI remote provider. By this, you can seamlessly integrate any
NCBI resource (reference genome, gene/protein sequences, ...) as
input file. Changed
- Snakemake now detects if automatically generated conda environments
have to be recreated because the workflow has been moved to a new
path.
- Remote functionality has been made more robust, in particular to
avoid race conditions.
- `--config` parameter evaluation has been fixed for non-string types.
- The Snakemake docker container is now based on the official debian
image.

Added

- Support for RMarkdown (.Rmd) in script directives.
- New option --debug-dag that prints all decisions while building the
DAG of jobs. This helps to debug problems like cycles or unexpected
MissingInputExceptions.
- New option --conda-prefix to specify the place where conda
environments are stored.

Changed

- Benchmark files now also include the maximal RSS and VMS size of the
Snakemake process and all sub processes.
- Speedup conda environment creation.
- Allow specification of DRMAA log dir.
- Pass cluster config to subworkflow.

Changed

- Fixed fix handling of local URIs with the wrapper directive.