# Ignore any folder named 'archive' anywhere
**/archive/

# Ignore all .DS_Store files
.DS_Store

# Ignore SIRIUS project file
lcms/sirius/pipernet.sirius

# Ignore everything inside rnaseq except assemblies folder
rnaseq/*
!rnaseq/assemblies/

# Inside assemblies, ignore all subfolders' contents except explicitly allowed files
rnaseq/assemblies/*/*
rnaseq/assemblies/*/aurum_data/
rnaseq/assemblies/*/pnigrum_genome/

# But do not ignore these specific files/folders in assemblies
!rnaseq/assemblies/*/busco_report.txt
!rnaseq/assemblies/*/transcriptome_expression_isoform.tsv
!rnaseq/assemblies/*/transcriptome.fasta
!rnaseq/assemblies/*/transcriptome.pep
!rnaseq/assemblies/*/annotations/