Continuous Integration is set

But at what cost?

Install with mamba seems to be required now. No problem on that, just sad for conda
MetaQUAST does not download references for now - in the future, it will become argument, so CI can happen on assembly

Can now run all parts without replicates (except DE analysis)

MOSCA cannot be run without replicates, but now the partial running of its functionalities is possible in all steps except for differential expression

• added option --no-differential-expression to reporter script, set if haven't performed differential expression analysis

Memory is now read in Gb

Several fixes in reporter columns

Option for downloading CDD resources

New option added for configuration: download_cdd.

• to be used if MOSCA has already been run once
• removes the --download-resources parameter from reCOGnizer's command
• also impacts the downloading of the other resources of reCOGnizer

Fixed mismanagement of read fixing

Reads fixed after rRNA removal were being trimmed in the last 2 characters of read name. This is now fixed.

Also, MOSCA now removes reads with less than 20 nucleotides after adapter removal, to avoid the spam from SortMeRNA.

Reimplemented fixing of reads after rRNA removal of paired-end

After unmerging reads, sometimes they will come messed up in a variety of ways:

• preprocessing removes reads messed up (not four lines long)
• also removes orphans - reads with their pair missing

Minor fix in adapter removal

Adapter removal now considers the "Adapter content" module of FastQC

Run MT without MG

Run MT without MG

• MOSCA is now capable of running MT without MG
• Combined with approach to not use assembly
• In the future might implement the use of assembly to analyze MT alone

Also added rejected and accepted files from rRNA removal to list of files to delete at preprocessing

Names can be customized

Names can be customized

• also several fixes on preprocessing of SE reads
• several methods for metaproteomics with Compomics software, still not reachable
• MINLEN and AVGQUAL now directly set from parameters
• shell commands now printed

Also several adaptations to reCOGnizer version 1.4

Several major fixes concerning snakemake integration

• scripts now called from the Snakefile directory
• added taxonomic and proteomics analysis tools
• added unlock option to mosca's main script
• adapted several methods for MEGAHIT use
• added bash script for downloading adapters and rRNA databases
• now accepts experiments files in EXCEL format
• config files from MOSGUITO now work integrally

Snakemake's integration into MOSCA

• MOSCA's main script is now wrapper to Snakefile
• Snakefile reads from config file, specified through the main script
• Experiments file specifies all information from --files, --samples and --conditions
• Removed all legacy scripts (tools' specific classes) except for rnaseqsimer and reab (to be removed in the future)
• mosca_tools no longer in classes - all functions