
.DS_Store
**/*.rds
bbsplit/*.stats.txt
*/bbsplit/*.stats.txt
fastqc/*/*.{html,zip}
fastqc/*_fastqc.{html,zip}
fq_lint/*/*.fq_lint.txt
hisat2/log/*.hisat2.summary.log
kallisto/*/abundance.{h5,tsv}
kallisto/*/kallisto_quant.log
kallisto/*/run_info.json
kallisto/kallisto.merged.gene_counts.tsv
kallisto/kallisto.merged.gene_counts_length_scaled.tsv
kallisto/kallisto.merged.gene_counts_scaled.tsv
kallisto/kallisto.merged.gene_lengths.tsv
kallisto/kallisto.merged.gene_tpm.tsv
kallisto/kallisto.merged.transcript_counts.tsv
kallisto/kallisto.merged.transcript_lengths.tsv
kallisto/kallisto.merged.transcript_tpm.tsv
multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
multiqc/multiqc_data/multiqc.parquet
multiqc/multiqc_data/multiqc.log
multiqc/multiqc_data/multiqc_data.json
multiqc/multiqc_data/multiqc_sources.txt
multiqc/multiqc_data/multiqc_software_versions.txt
multiqc/multiqc_data/llms-full.txt
multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
multiqc/multiqc_report.html
pipeline_info/*.{html,json,txt,yml}
bowtie2_rrna/*.bowtie2.log
bowtie2_salmon/*.bowtie2.log
bowtie2_salmon/log/*.bowtie2.log
ribodetector/*.log
sortmerna/*.sortmerna.log
star_rsem/*.stat/*.{cnt,model,theta}
star_rsem/*.{genes,isoforms}.results
star_rsem/log/*.log
star_{salmon,rsem}/log/*.Log.{final.out,out,progress.out}
trimgalore/*fastq.gz_trimming_report.txt
umitools/*.umi_extract.log
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/*.{bam,bam.bai}
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/bigwig/*.bigWig
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/dupradar/gene_data/*_dupMatrix.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/dupradar/histogram/*_expressionHist.pdf
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/dupradar/intercepts_slope/*_intercept_slope.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/featurecounts/*.featureCounts.{txt,tsv}.summary
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/picard_metrics/*.metrics.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/qualimap/*/css/*
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/qualimap/*/images_qualimapReport/*
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/qualimap/*/qualimapReport.html
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/qualimap/*/raw_data_qualimapReport/*
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/qualimap/*/rnaseq_qc_results.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rseqc/bam_stat/*.bam_stat.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rseqc/read_distribution/*.read_distribution.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/*
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats}
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/dupradar/box_plot/*_duprateExpBoxplot.{png,svg}
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/dupradar/gene_data/*_dupMatrix.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/dupradar/histogram/*_expressionHist.{png,svg}
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/dupradar/intercepts_slope/*_intercept_slope.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/dupradar/scatter_plot/*_duprateExpDens.{png,svg}
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/dupradar/*_mqc.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/featurecounts/*.featureCounts.tsv.summary
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/qualimap/*/images_qualimapReport/*
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/qualimap/*/qualimapReport.html
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/qualimap/*/raw_data_qualimapReport/*
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/qualimap/*/rnaseq_qc_results.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/rseqc/bam_stat/*.bam_stat.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/rseqc/read_distribution/*.read_distribution.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,plot,rscript,txt,xls}/*
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/rustqc/samtools_stats/*.{flagstat,idxstats,stats}
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/stringtie/*.ballgown/t_data.ctab
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/stringtie/*.gene.abundance.txt
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/stringtie/*.{coverage,transcripts}.gtf
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/stringtie/stringtie_merge.gtf
{hisat2,star_rsem,star_salmon,bowtie2_salmon}/{umitools,umicollapse}/{genomic,transcriptomic}_dedup_log/*.log
{multiqc,multiqc/**}/.stub
{multiqc,multiqc/**}/multiqc_report.html
{multiqc,multiqc/**}/multiqc_report_data/multiqc.parquet
{multiqc,multiqc/**}/multiqc_report_data/fastqc_filtered*.txt
{multiqc,multiqc/**}/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_fastqc_fastqc_filtered.txt
{multiqc,multiqc/**}/multiqc_report_data/hisat2_pe_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/hisat2_se_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt
{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt
{multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt
{multiqc,multiqc/**}/multiqc_report_data/llms-full.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc.log
{multiqc,multiqc/**}/multiqc_report_data/multiqc_data.json
{multiqc,multiqc/**}/multiqc_report_data/multiqc_dupradar.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_fail_strand_check_table.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_general_stats.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_hisat2.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_kallisto.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_picard_dups.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_rsem.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_bam_stat.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_infer_experiment.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_junction_annotation.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_read_distribution.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_salmon.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_salmon_deseq2_clustering.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_salmon_deseq2_pca.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_sample-relationships*.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_software_versions.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_bowtie2_rrna.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_bowtie2_bowtie2_rrna.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_cutadapt.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_ribodetector.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_sortmerna.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_sources.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_star.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_kraken.txt
{multiqc,multiqc/**}/multiqc_report_data/kraken-top-n-plot.txt
{multiqc,multiqc/**}/multiqc_report_data/bbmap-bbsplit_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/bbmap.txt
{multiqc,multiqc/**}/multiqc_report_data/bbsplit_stats_table.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_star_rsem_deseq2_clustering.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_star_rsem_deseq2_pca.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_star_salmon_deseq2_clustering.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_star_salmon_deseq2_pca.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_umitools_dedup.txt
{multiqc,multiqc/**}/multiqc_report_data/picard_deduplication.txt
{multiqc,multiqc/**}/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt
{multiqc,multiqc/**}/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt
{multiqc,multiqc/**}/multiqc_report_data/qualimap_genomic_origin.txt
{multiqc,multiqc/**}/multiqc_report_data/qualimap_rnaseq_cov_hist.txt
{multiqc,multiqc/**}/multiqc_report_data/qualimap_rnaseq_genome_results.txt
{multiqc,multiqc/**}/multiqc_report_data/rsem_assignment_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/rsem_multimapping_rates.txt
{multiqc,multiqc/**}/multiqc_report_data/rseqc_bam_stat.txt
{multiqc,multiqc/**}/multiqc_report_data/rseqc_inner_distance*.txt
{multiqc,multiqc/**}/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt
{multiqc,multiqc/**}/multiqc_report_data/rseqc_read_*.txt
{multiqc,multiqc/**}/multiqc_report_data/salmon_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/samtools-flagstat-dp_*.txt
{multiqc,multiqc/**}/multiqc_report_data/samtools-flagstat-pct-table.txt
{multiqc,multiqc/**}/multiqc_report_data/samtools-flagstat-table.txt
{multiqc,multiqc/**}/multiqc_report_data/samtools-stats-dp.txt
{multiqc,multiqc/**}/multiqc_report_data/samtools_alignment_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/bowtie2_pe_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/bowtie2_se_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_bowtie2.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_bowtie2_salmon_deseq2_clustering.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_bowtie2_salmon_deseq2_pca.txt
{multiqc,multiqc/**}/multiqc_report_data/bowtie2_rrna-*.txt
{multiqc,multiqc/**}/multiqc_report_data/ribodetector-*.txt
{multiqc,multiqc/**}/multiqc_report_data/sortmerna-detailed-plot.txt
{multiqc,multiqc/**}/multiqc_report_data/star_alignment_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/star_summary_table.txt
{multiqc,multiqc/**}/multiqc_report_data/umitools_deduplication_barplot.txt
{multiqc,multiqc/**}/multiqc_report_data/umitools_stats_violin.txt
{multiqc,multiqc/**}/multiqc_report_data/picard_MeanQualityByCycle_histogram_1.txt
{multiqc,multiqc/**}/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg}
# Per-sample output patterns (skip_quantification_merge mode)
# These outputs land under <sample>/multiqc/<sample>_multiqc_report_data/ etc.
**/fastqc/**/*.{html,zip}
**/fq_lint/**/*.fq_lint.txt
**/*_multiqc_report.html
**/*_multiqc_report_data/multiqc.parquet
**/*_multiqc_report_data/multiqc.log
**/*_multiqc_report_data/multiqc_data.json
**/*_multiqc_report_data/multiqc_sources.txt
**/*_multiqc_report_data/multiqc_software_versions.txt
**/*_multiqc_report_data/multiqc_salmon.txt
**/*_multiqc_report_data/multiqc_general_stats.txt
**/*_multiqc_report_data/multiqc_cutadapt.txt
**/*_multiqc_report_data/multiqc_fastqc_fastqc_filtered.txt
**/*_multiqc_report_data/llms-full.txt
**/*_multiqc_report_data/fastqc_filtered*.txt
**/*_multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt
**/*_multiqc_report_data/fastqc_sequence_length_distribution_plot.txt
**/*_multiqc_report_data/bbmap-bbsplit_plot.txt
**/*_multiqc_report_data/bbmap.txt
**/*_multiqc_report_data/bbsplit_stats_table.txt
**/*_multiqc_report_data/salmon_plot.txt
**/*_multiqc_report_data/multiqc_sample-relationships*.txt
**/*_multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg}
# Per-sample salmon/tximport outputs (skip_quantification_merge mode)
*/salmon/*.gene_counts.tsv
*/salmon/*.gene_counts_scaled.tsv
*/salmon/*.gene_lengths.tsv
*/salmon/*.gene_tpm.tsv
*/salmon/*.transcript_counts.tsv
*/salmon/*.transcript_lengths.tsv
*/salmon/*.transcript_tpm.tsv
*/salmon/*/aux_info/fld.gz
*/salmon/*/aux_info/meta_info.json
*/salmon/*/libParams/flenDist.txt
*/salmon/*/logs/salmon_quant.log
*/salmon/*/quant.genes.sf
*/salmon/*/quant.sf
**/*_trimming_report.txt
{salmon,star_rsem,star_salmon,bowtie2_salmon}/deseq2_qc/R_sessionInfo.log
{salmon,star_rsem,star_salmon,bowtie2_salmon}/deseq2_qc/deseq2.dds.RData
{salmon,star_rsem,star_salmon,bowtie2_salmon}/deseq2_qc/deseq2.pca.vals.txt
{salmon,star_rsem,star_salmon,bowtie2_salmon}/deseq2_qc/deseq2.plots.pdf
{salmon,star_rsem,star_salmon,bowtie2_salmon}/deseq2_qc/deseq2.sample.dists.txt
{salmon,star_rsem,star_salmon,bowtie2_salmon}/deseq2_qc/size_factors/*.txt
{salmon,star_rsem,star_salmon,bowtie2_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData
{salmon,star_rsem,star_salmon,bowtie2_salmon}/umitools/prepare_for_quantification_log/*
{salmon,star_rsem,star_salmon,bowtie2_salmon}/umitools/{genomic,transcriptomic}_dedup_log/*
{salmon,star_salmon,bowtie2_salmon}/*/aux_info/fld.gz
{salmon,star_salmon,bowtie2_salmon}/*/aux_info/meta_info.json
{salmon,star_salmon,bowtie2_salmon}/*/libParams/flenDist.txt
{salmon,star_salmon,bowtie2_salmon}/*/logs/salmon_quant.log
{salmon,star_salmon,bowtie2_salmon}/*/quant.genes.sf
{salmon,star_salmon,bowtie2_salmon}/*/quant.sf
{salmon,star_salmon,bowtie2_salmon}/salmon.merged.gene_counts.tsv
{salmon,star_salmon,bowtie2_salmon}/salmon.merged.gene_counts_length_scaled.tsv
{salmon,star_salmon,bowtie2_salmon}/salmon.merged.gene_counts_scaled.tsv
{salmon,star_salmon,bowtie2_salmon}/salmon.merged.gene_lengths.tsv
{salmon,star_salmon,bowtie2_salmon}/salmon.merged.gene_tpm.tsv
{salmon,star_salmon,bowtie2_salmon}/salmon.merged.transcript_counts.tsv
{salmon,star_salmon,bowtie2_salmon}/salmon.merged.transcript_lengths.tsv
{salmon,star_salmon,bowtie2_salmon}/salmon.merged.transcript_tpm.tsv
{star_salmon,star_rsem,hisat2}/contaminants/kraken2/kraken_reports/*.kraken2.report.txt
