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# ==================
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# System & Temporary
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# ==================
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# Any folder named 'archive' anywhere
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**/archive/
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# Ignore all .DS_Store files
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.DS_Store
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# ==========
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# LC-MS Data
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# ==========
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# SIRIUS project file
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lcms/sirius/pipernet.sirius
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# LC-MS data preparation outputs
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lcms/ftable_clean.csv
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lcms/ntable_clean.csv
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# ============
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# RNA-Seq Data
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# ============
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# Everything inside rnaseq except assemblies folder
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rnaseq/*
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!rnaseq/assemblies/
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!rnaseq/orthogroups/
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# Inside assemblies, ignore all subfolders' contents except explicitly allowed files
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rnaseq/assemblies/*/*
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rnaseq/assemblies/*/aurum_data/
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rnaseq/assemblies/*/pnigrum_genome/
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# But do not ignore these specific files/folders in assemblies
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!rnaseq/assemblies/*/busco_report.txt
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!rnaseq/assemblies/*/transcriptome_expression_isoform.tsv
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!rnaseq/assemblies/*/transcriptome.fasta
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!rnaseq/assemblies/*/transcriptome.pep
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!rnaseq/assemblies/*/annotations/
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