Add unit tests for critical functions

[Nicolai-vKuegelgen]

Unit tests missing for functions used in R process_CNV_calls

• R I/O functions
  • gtf & genome info loading
  • [ ] get_chromosome_set (should be redone)
  • get_sample_info (maybe redo)
  • CNV readers; redo after change to VCF
  • static data path management (move to report functions?)
  • CNV table format / scheme
• call (pre) filter & merge
• combined CNV callers
• annotate reference overlap
• annotate impact lists
• annotate array features
• annotate Check-Score
  • Check-Score
  • Precision Estimation

Unit tests missing for snakemake input functions

• get_tool_filter_settings
• get_tool_resource
• fix_container_path (refactor/combined with staticdata smk)
• get_target_files
• get_chip
• get_ref_id
• get_preprocess_input
• get_report_sample_input
• get_cnv_vcf_output

Unit tests missing for main app

• helper functions
  • read_sample_table (helper)
  • collect_SNP_cluster_ids (helper)
  • Misc
• check_sample_table (replace with scheme validation?)
• check_config (replace with scheme validation?)
• make_singularity_args ( re: fix_container_path )
• [ ] make_PennCNV_sexfile
• copy_setup_files
• create_missing_staticdata
• run_snakemake
• setup_argparse