.DS_Store
Ancient_DNA/pydamage/analyze/*/*.csv
Ancient_DNA/variant_calling/*/*.vcf.gz
Annotation/Prokka/**/*.{err,gbk,log,sqn}
Annotation/Prokka/**/*.tmp.*
Assembly/*/*.log
Assembly/*/QC/*/*.bowtie2.log
Assembly/*/QC/*/QUAST/*.{pdf,html,log}
Assembly/*/QC/*/QUAST/**/*.{pdf,html,log}
Assembly/*-pypolca/*/*.vcf
Assembly/MEGAHIT/QC/*/*.bowtie2.log
GenomeBinning/CONCOCT/stats/*_{original,PCA_components,PCA_transformed}_data_gt1000.csv
GenomeBinning/CONCOCT/stats/*_log.txt
GenomeBinning/CONCOCT/stats/*.tsv
GenomeBinning/DASTool/*.log
GenomeBinning/depths/**/*-depth.txt.gz
GenomeBinning/depths/bins/*.png
GenomeBinning/QC/busco_summary.tsv
GenomeBinning/QC/BUSCO/**/.checkpoint
GenomeBinning/QC/BUSCO/**/{logs,prodigal_output,busco_sequences,hmmer_output}/**
GenomeBinning/QC/BUSCO/**/*.{json,log,txt}
GenomeBinning/QC/BUSCO/**/short_summary*.{txt,json}
GenomeBinning/QC/BUSCO/*/*{-busco.log,-busco.batch_summary.txt}
GenomeBinning/QC/CheckM/*/{checkm.log,lineage.ms}
GenomeBinning/QC/CheckM/*/bins/*/hmmer.{analyze,tree}.txt
GenomeBinning/QC/CheckM/*/storage/**
GenomeBinning/QC/CheckM2/**/DIAMOND_RESULTS.tsv
GenomeBinning/QC/CheckM2/*/checkm2.log
GenomeBinning/QC/QUAST/*/*.{pdf,html,log}
GenomeBinning/QC/QUAST/*/**/*.{pdf,html,log}
GenomeBinning/SemiBin2/log/*.log
multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
multiqc/multiqc_data/llms-full.txt
multiqc/multiqc_data/multiqc_data.json
multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_data/multiqc_software_versions.yaml
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_data/multiqc_sources.yaml
multiqc/multiqc_data/multiqc.log
multiqc/multiqc_data/multiqc.parquet
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
pipeline_info/*.{html,json,txt,yml}
QC_longreads/NanoLyse/*.log
QC_longreads/NanoPlot/**/*.{html,png}
QC_shortreads/fastp/**/*.html
QC_shortreads/fastqc/*_fastqc.{html,zip}
QC_shortreads/remove_phix/*.log
Taxonomy/CAT/**/*.log
Taxonomy/GTDB-Tk/**/*.log
Taxonomy/GTDB-Tk/**/gtdbtk.json
VirusIdentification/geNomad/**/*_aggregated_classification.tsv
