What's Changed

• Specify Python in requirements.yml to solve mamba solving issue by @KatSteinke in #20:
  The base environment in requirements.yml did not specify a Python version. This led to issues resolving it when running the recommended command for environment creation in mamba. The requirements file has therefore been updated to specify Python 3.10.

• Fix handling of several optional arguments in run_pipeline.py by @KatSteinke in #22:
  Starting the pipeline failed if no flags were specified under --snake_flags even though there no longer is anything that needs to be set this way. A default has been set to handle this.
  Additionally, the argument to supply a custom config file was referenced incorrectly. This has now been corrected.

• Fix setting custom error profile for CAMISIM by @KatSteinke in #23:
  The defaults for custom error profiles were set in a way that could lead to the pipeline incorrectly assuming a custom error profile had been specified. The way the defaults are set in the Snakefile, as well as how the command for starting the workflow is generated, have been adapted to prevent this.

Full Changelog: v1.1.1...v1.1.2

What's Changed

• Improve README by @KatSteinke in #17

Full Changelog: v1.1.0...v1.1.1

What's Changed

• Allow user to specify input file rather than hardcoding by @KatSteinke in #9
• Add test run functionality by @KatSteinke in #11
• Specify requirements as separate environment by @KatSteinke in #12
• Specify cores more nicely by @KatSteinke in #14
• Add config with defaults by @KatSteinke in #15

Full Changelog: v1.0...v1.1.0

Initial release of MAGICIAN: a basic Snakemake workflow for simulating metagenome-assembled genomes with dependency management using conda/mamba.