katsteinke / magician Goto Github PK

When using mamba and specifying both conda-forge and defaults channels in an environment specification, mamba can fail to solve the environment. This has caused issues when installing the base environments.

Fix rules that (used to) depend on Singularity with conda environment equivalents.

Handle the input file selection more nicely - allow the user to specify which file to use in the wrapper and pass through to Snakemake as a config parameter.

Create a conda environment specification for MAGICIAN.

The handling of custom profile basenames or their absence can break. Handle this better than with the bool/string kludge.

Add an ability to perform a test run from the wrapper; include a test dataset and (roughly) expected output for this.

Config file handling is broken in run_pipeline.py (wrong argument name)

Currently the CAMISIM path needs to be set in the Snakefile - maybe include a small config file, that's a bit more reasonable for people to expect to alter. In the future, might want to move to the newest version of CAMISIM to avoid the issue altogether.

duplicate of #1

Set a default conda frontend for Snakemake (since conda/mamba are required anyway).

Currently the amount of cores for Snakemake has to be specified using --snake_flags in run_magician.py - it would be nicer if there were a preset (and --snake_flags could be left blank).