Snakemake

Changed

- Fixed several bugs in reports and scheduler.
- Remove automatic (but buggy) encoding of csv/tsv files into HTML
tables in the report (we will soon have a better alternative).
- Fixed bug in kubernetes executor occurring with large source files.

Added

- Execution backend for GA4GH TES (task execution scheduler) an
abstraction layer for various cluster and cloud queuing systems
(svedziok, uniqueg).
- script, notebook, wrapper and cwl directives now permit to use
wildcards and params for composing paths (johanneskoester).

Changed

- Restored compatibility with Python 3.5 and 3.6 (cclienti).
- Various usability bug fixes (goi43, johanneskoester, dcroote).
- Better and more secure parsing of values when using --config
(bingxiao).

Changed

- Further speed improvements for DAG computation.
- Fixed metadata migration errors occurring with long output file
paths.
- Add WorkflowHub specifications to the docs.
- Fix group assignments.

Changed

- Added missing files to source distribution.

Changed

- DAG computation runtime has been improved by orders of magnitude, it
is linear in the number of jobs now (mhulsmann, johanneskoester).
- Stat calls have been dramatically reduced and are now performed in
parallel (johanneskoester).
- Scheduler fixes (FelixMoelder).
- Directory support and other fixes for Google Life Sciences backend
(vsoch, millerdz).
- Support for panoptes monitor server (fgypas).
- Extended pathlib support (mbhall88).
- Vim plugin improvements (troycomi).
- Prevent jobs being rerun when input files are marked as ancient and
another job in the DAG creates them.
- Fixed --list-code-changes for included rules (jbloom).

Added

- Syntax highlighting for nano (baileythegreen).

Changed

- Use coin ILP solver for scheduling by default (GLPK has bugs that
can cause it to fail in certain situations).
- If coin is not available, fall back to greedy scheduler.