LICENSE, linting and other minor updates

[FerriolCalvet]

This PR updates:

• LICENSE to AGPLv3 with slight modification
• Linting of config files
• Define GNOMAD variant allele frequency threshold from nextflow.config
• Update INDEL size to 50, bigger than that will be structural variants

We will wait for Tiago's approval on the LICENSE to merge this PR.

AI summary

This pull request primarily updates the licensing of the repository, clarifies usage terms, and standardizes configuration and process naming conventions across multiple config files. Additionally, it introduces minor improvements and cleanups in parameter handling and output formatting.

Licensing and Usage Terms:

• Updated the LICENSE file to specify the software is under the GNU Affero General Public License v3 (AGPLv3), restricts use to academic and non-commercial purposes, and clarifies copyright ownership by IRB Barcelona.

Configuration and Naming Standardization:

• Standardized process withName declarations in conf/modules.config by removing unnecessary quotes and making naming consistent throughout, improving maintainability and clarity. [1] [2] [3] [4] [5] [6] [7] [8]

Parameter Handling and Output Formatting:

• Improved filter and output formatting logic in several processes (e.g., CLEANMUTATIONS, SOMATICMUTATIONS, SUBSETMUTPROFILE), making them more robust and easier to read. [1] [2]
• Added new parameters for annotation filtering in SUMANNOTATION (e.g., gnomad_af_threshold, underscore).

Minor Configuration Cleanups:

• Fixed path interpolation and formatting in conf/mice.config and removed redundant blank lines in various config files for better readability. [1] [2] [3] [4] [5] [6] [7] [8]

These changes collectively improve the clarity, usability, and legal compliance of the repository.