Reintroduction of MOSCA into Bioconda

Reintroduction of MOSCA into Bioconda

Since MOSCA 1.3.6, the list of dependencies of the pipeline has become too complex for conda to manage.
This release makes use of snakemake environments to simplify the minimal environment required to install MOSCA. MOSCA ow only requires snakemake.

Now MOSCA uses snakemake's rules

All the rules have been moved to corresponding .smk files. This has simplified a lot the main script.
Script files can no longer be run through the command line, however. Interface is with snakemake directly.
First step into producing a web-service.

Added schema for validating config.json

config.schema.yaml checks if all needed informations are present, and in correct format, on the input config file.

New parameter

metaproteomics_add_reference_proteomes: New option for not searching for reference proteomes for organisms identified. Helps save a lot of time during Peptide-to-Spectrum Matching.

Tests have been reformatted

Complete MGMP has been reintroduced, however, it still fails for too much disk usage. It'll be a problem for another time.

Several fixes and improvements

params.method was not being correctly read on de_analysis.R.
config.json is now explicitly required.
tmp directory when handling SortMeRNA is created inside SortMeRNA output directory.
Removed pandas warnings concerning reading files without low_memory=False.
Memory allocated in metaproteomics now in G instead of M.
Removed UPIMAPI apt dependencies - are no longer needed.
Fix on reading method for normalization.
Fix on parsing conditions in de_analysis.R.