.gitignore

# General
.gitignore
**/__pycache__


#Snakemake results
/shallow-shotgun-analysis-workflow/results/config/config.yml
/shallow-shotgun-analysis-workflow/results/config/samples.yml
#exclude everything
/shallow-shotgun-analysis-workflow/results/*
/shallow-shotgun-analysis-workflow/resources/*
shallow-shotgun-analysis-workflow/workflow/.snakemake/*
.snakemake

#old_versions
/shallow-shotgun-analysis-workflow/workflow/old

#exceptopion to the rule
!/shallow-shotgun-analysis-workflow/results/.gitkeep
!/shallow-shotgun-analysis-workflow/resources/.gitkeep
!/shallow-shotgun-analysis-workflow/resources/images/step1-dag.png

REDCAP/

# Parsers module
parsers/data/*
parsers/.empty
parsers/.vscode
parsers/REDCAP
parsers/ncbr_covid
parsers/upload.csv
parsers/db_pass.json
parsers/processed.csv

# Additional modules
FTP_DATA/
ILLUMINA_CLIENT/
data/
notebooks/

# Analysis
notebooks/lab_result_analysis/config.json
**/db_pass
.vscode
parsers/summary.csv
parsers/summary.csv