preprocessing/fastqc/*.{html,zip}
preprocessing/fastp/*.{html,log}

multiqc/multiqc_data/**
multiqc/multiqc_data/*.{log,json}
multiqc/multiqc_data/multiqc_general_stats.txt
multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
multiqc/multiqc_data/homer_tagdir.txt
multiqc/multiqc_data/rseqc_read_dups.txt
multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_report.html
multiqc/multiqc_plots/**
multiqc/multiqc_plots/{pdf,png,svg}/*.{pdf,png,svg}
pipeline_info/*.{html,json,txt,yml}

*/alignments/logs/*.txt
star/log/*.Log.{final.out,out,progress.out}
star/star/Log.out
hisat2/log/*.hisat2.summary.log
*/deduplicated/logs/*.txt
*/{reports,summary}/*.{html,txt}
**/*.command.log
**/*.bedGraph.gz
**/tagInfo.txt
**/*.{bam,bai}
**/*.featureCounts.txt
**/*.featureCounts.txt.summary
**/*.pdf

transcript_identification/homer/*_tagdir/*
transcript_identification/filtered/*_filtered.bed
transcript_identification/intersect/*_intersect.bed
transcript_identification/grohmm/*.tdFinal.txt
transcript_identification/grohmm/*.tdFinal_mqc.csv
transcript_identification/grohmm/*.tdplot_mqc.png

quality_control/bbsplit/*.stats.txt
quality_control/**
**/DupRate_plot.pdf
