.gitignore

# all backup emacs and vim files
*~

# mac files
.DS_Store
._*

# Python cached data
__pycache__/

# snakemake internal directories
.snakemake

# snakemake DAGs
dag.pdf

# pipeline-execution-related
.cache
.java

# Python-generated MAPP config file
configs/config.yml

# pipeline summary + summary logs
summary/
summary.tar.gz
logs/

# all the default output diretories for separate modules
modules/PREPROCESSING/output
modules/CREATE_SITECOUNT_MATRICES/output
modules/EXTRACT_AS_EXONS/output
modules/PREPARE_TANDEM_PAS/output
modules/QUANTIFICATION/output
modules/PAQR/output
modules/MAEI/output
modules/KAPAC/output
modules/REPORT_RESULTS/output

# configuration files for dev purposes
configs/test_config_template.yml
modules/CREATE_SITECOUNT_MATRICES/configs/test_config.yml
modules/EXTRACT_AS_EXONS/configs/test_config.yml
modules/KAPAC/configs/test_config.yml
modules/MAEI/configs/test_config.yml
modules/PAQR/configs/test_config.yml
modules/PREPARE_TANDEM_PAS/configs/test_config.yml
modules/PREPROCESSING/configs/test_config.yml
modules/QUANTIFICATION/configs/test_config.yml
modules/REPORT_RESULTS/configs/test_config.yml

# test dataset from zenodo
MAPP_test_data