jashapiro
commented
3 weeks ago Copying suggested additions from Slack:
# Ignore large (or linked) data and reference files for all modules
*/data/*
*/QC/*
*/index/*
# Ignore RDS results files
*/results/**/*.rds
# But we want to include the QC reports for the sample we ran
# gitignore is odd in how it checks which files to include in nested directories,
# so we have to do some odd stuff
!RNA-seq/QC/gastric-cancer
RNA-seq/QC/gastric-cancer/fastp/*
RNA-seq/QC/gastric-cancer/fastqc/*
!RNA-seq/QC/gastric-cancer/**/SRR585570
When creating gitignore.user, I forgot to pay attention to the individual module gitignore files... which means we are not ignoring data files. That's bad. We want to ignore those, but we probably don't want to ignore everything in the data folders and all the same things that we ignore in the main repository.