Refactoring: remove large files from tracking and update code with multimodal DBG

Author: marcoreverenna

.gitignore

@@ -1,39 +1,28 @@
 # folders
+_archive/
+inputs/
+fasta/
+dist/
 outputs/
-outputs_notebook/
 figures/
+benchmark/
 logs/
-nextflow/
 work/
 examples/outputs/
-.ipynb_checkpoints/
-.vscode/
 docs/build/
-_archive/
 
 # ignore compiled python files
 *.pyc
+*.egg-info/
 __pycache__/
 .DS_Store
+.ipynb_checkpoints/
+.vscode/
 
 # files
-inputs/*
-inputs/BIND15.csv
-inputs/BIND16.csv
-inputs/ma2.csv
-inputs/ma3.csv
-inputs/NB1.csv
-inputs/NB2.csv
-inputs/NB3.csv
-inputs/NB4.csv
-inputs/NB5.csv
-inputs/NB8.csv
-inputs/NB12.csv
-inputs/NB13.csv
-inputs/pa.csv
-inputs/pb.csv
-
+*.csv
+*.xlsx
 examples/*.svg
 docs/source/tutorials/case_studies/*.csv
 docs/source/tutorials/case_studies/notebook_results/
-docs/source/tutorials/case_studies/summary_tables/*
+docs/source/tutorials/case_studies/summary_tables/*