The Pipeline generally output three directories: data, references and results the tree output of each will look like below. data: data ├── fastp │   ├── SRR27410792 │   │   ├── SRR27410792_fastp.html │   │   ├── SRR27410792_fastp.json │   │   ├── SRR27410792_trimmed_R1.fastq.gz │   │   └── SRR27410792_trimmed_R2.fastq.gz │   └── SRR453566 │   ├── SRR453566_fastp.html │   ├── SRR453566_fastp.json │   ├── SRR453566_trimmed_R1.fastq.gz │   └── SRR453566_trimmed_R2.fastq.gz └── raw ├── SRR27410792 │   ├── SRR27410792_1.fastq.gz │   └── SRR27410792_2.fastq.gz └── SRR453566 ├── SRR453566_1.fastq.gz └── SRR453566_2.fastq.gz 7 directories, 12 files references: references └── saccer3 ├── chromsizes │   └── saccer3.chrom.sizes ├── fasta │   ├── Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz │   └── unzipped.fa ├── gtf │   ├── Saccharomyces_cerevisiae.R64-1-1.108.gtf.gz │   └── unzipped.gtf └── indexes ├── STAR │   ├── Genome │   ├── Log.out │   ├── SA │   ├── SAindex │   ├── chrLength.txt │   ├── chrName.txt │   ├── chrNameLength.txt │   ├── chrStart.txt │   ├── exonGeTrInfo.tab │   ├── exonInfo.tab │   ├── geneInfo.tab │   ├── genomeParameters.txt │   ├── sjdbInfo.txt │   ├── sjdbList.fromGTF.out.tab │   ├── sjdbList.out.tab │   └── transcriptInfo.tab └── bowtie2 ├── saccer3.1.bt2 ├── saccer3.2.bt2 ├── saccer3.3.bt2 ├── saccer3.4.bt2 ├── saccer3.rev.1.bt2 └── saccer3.rev.2.bt2 8 directories, 27 files results: results ├── atac │   ├── ATAC-Test-Run │   │   └── SRR27410792 │   │   ├── alignment │   │   │   ├── SRR27410792.bowtie2.log │   │   │   ├── SRR27410792_final_sorted.bam │   │   │   ├── SRR27410792_final_sorted.bam.bai │   │   │   ├── SRR27410792_sorted_dedup.txt │   │   │   ├── filtered.bam │   │   │   ├── sorted.bam │   │   │   └── sorted_dedup.bam │   │   ├── homer │   │   │   └── tagdir │   │   │   ├── I.tags.tsv │   │   │   ├── II.tags.tsv │   │   │   ├── III.tags.tsv │   │   │   ├── IV.tags.tsv │   │   │   ├── IX.tags.tsv │   │   │   ├── Mito.tags.tsv │   │   │   ├── V.tags.tsv │   │   │   ├── VI.tags.tsv │   │   │   ├── VII.tags.tsv │   │   │   ├── VIII.tags.tsv │   │   │   ├── X.tags.tsv │   │   │   ├── XI.tags.tsv │   │   │   ├── XII.tags.tsv │   │   │   ├── XIII.tags.tsv │   │   │   ├── XIV.tags.tsv │   │   │   ├── XV.tags.tsv │   │   │   ├── XVI.tags.tsv │   │   │   ├── genomeGCcontent.txt │   │   │   ├── tagAutocorrelation.txt │   │   │   ├── tagCountDistribution.txt │   │   │   ├── tagFreq.txt │   │   │   ├── tagFreqUniq.txt │   │   │   ├── tagGCcontent.txt │   │   │   ├── tagInfo.txt │   │   │   └── tagLengthDistribution.txt │   │   ├── peaks │   │   │   ├── SRR27410792_peaks.narrowPeak │   │   │   ├── SRR27410792_peaks.xls │   │   │   ├── SRR27410792_summits.bed │   │   │   ├── annotation │   │   │   │   └── SRR27410792.annotated.txt │   │   │   └── tmp_b_c.txt │   │   ├── qc │   │   │   ├── SRR27410792.flagstat │   │   │   ├── SRR27410792.frip.tsv │   │   │   ├── SRR27410792.insert_size_histogram.pdf -> /home/fchen3357/nf_work/0f/5e933790a49e64d47e2eb2bbb0647b/SRR27410792.insert_size_histogram.pdf │   │   │   ├── SRR27410792.insert_size_metrics.txt -> /home/fchen3357/nf_work/0f/5e933790a49e64d47e2eb2bbb0647b/SRR27410792.insert_size_metrics.txt │   │   │   ├── SRR27410792.peak_stats.tsv │   │   │   └── SRR27410792.stats │   │   └── visualization │   │   ├── SRR27410792.bw │   │   └── tagdir │   │   └── tagdir.ucsc.bedGraph.gz │   └── multiqc │   ├── alignment │   │   ├── multiqc_data │   │   │   ├── bowtie2_pe_plot.txt │   │   │   ├── llms-full.txt │   │   │   ├── multiqc.log │   │   │   ├── multiqc.parquet │   │   │   ├── multiqc_bowtie2.txt │   │   │   ├── multiqc_citations.txt │   │   │   ├── multiqc_data.json │   │   │   ├── multiqc_general_stats.txt │   │   │   ├── multiqc_picard_dups.txt │   │   │   ├── multiqc_picard_insertSize.txt │   │   │   ├── multiqc_samtools_flagstat.txt │   │   │   ├── multiqc_samtools_stats.txt │   │   │   ├── multiqc_software_versions.txt │   │   │   ├── multiqc_sources.txt │   │   │   ├── picard_MarkIlluminaAdapters_histogram.txt │   │   │   ├── picard_MeanQualityByCycle_histogram.txt │   │   │   ├── picard_MeanQualityByCycle_histogram_1.txt │   │   │   ├── picard_QualityScoreDistribution_histogram.txt │   │   │   ├── picard_deduplication.txt │   │   │   ├── picard_insert_size_Counts.txt │   │   │   ├── picard_insert_size_Percentages.txt │   │   │   ├── samtools-flagstat-pct-table.txt │   │   │   ├── samtools-flagstat-table.txt │   │   │   ├── samtools-stats-dp.txt │   │   │   └── samtools_alignment_plot.txt │   │   └── multiqc_report.html │   └── read │   ├── multiqc_data │   │   ├── fastp-insert-size-plot.txt │   │   ├── fastp-seq-content-gc-plot_Read_1_After_filtering.txt │   │   ├── fastp-seq-content-gc-plot_Read_1_Before_filtering.txt │   │   ├── fastp-seq-content-gc-plot_Read_2_After_filtering.txt │   │   ├── fastp-seq-content-gc-plot_Read_2_Before_filtering.txt │   │   ├── fastp-seq-content-n-plot_Read_1_After_filtering.txt │   │   ├── fastp-seq-content-n-plot_Read_1_Before_filtering.txt │   │   ├── fastp-seq-content-n-plot_Read_2_After_filtering.txt │   │   ├── fastp-seq-content-n-plot_Read_2_Before_filtering.txt │   │   ├── fastp-seq-quality-plot_Read_1_After_filtering.txt │   │   ├── fastp-seq-quality-plot_Read_1_Before_filtering.txt │   │   ├── fastp-seq-quality-plot_Read_2_After_filtering.txt │   │   ├── fastp-seq-quality-plot_Read_2_Before_filtering.txt │   │   ├── fastp_filtered_reads_plot.txt │   │   ├── fastqc-status-check-heatmap.txt │   │   ├── fastqc_adapter_content_plot.txt │   │   ├── fastqc_per_base_n_content_plot.txt │   │   ├── fastqc_per_base_sequence_quality_plot.txt │   │   ├── fastqc_per_sequence_gc_content_plot_Counts.txt │   │   ├── fastqc_per_sequence_gc_content_plot_Percentages.txt │   │   ├── fastqc_per_sequence_quality_scores_plot.txt │   │   ├── fastqc_sequence_counts_plot.txt │   │   ├── fastqc_sequence_duplication_levels_plot.txt │   │   ├── fastqc_sequence_length_distribution_plot.txt │   │   ├── llms-full.txt │   │   ├── multiqc.log │   │   ├── multiqc.parquet │   │   ├── multiqc_citations.txt │   │   ├── multiqc_data.json │   │   ├── multiqc_fastp.txt │   │   ├── multiqc_fastqc.txt │   │   ├── multiqc_general_stats.txt │   │   ├── multiqc_software_versions.txt │   │   └── multiqc_sources.txt │   └── multiqc_report.html └── rna ├── RNA-Test-Run │   └── SRR453566 │   ├── alignment │   │   ├── SRR453566.Aligned.sortedByCoord.out.bam │   │   ├── SRR453566.Aligned.sortedByCoord.out.bam.bai │   │   ├── SRR453566.Log.final.out │   │   ├── SRR453566.Log.out │   │   ├── SRR453566.Log.progress.out │   │   ├── SRR453566.SJ.out.tab │   │   ├── SRR453566_final_sorted.bam │   │   ├── SRR453566_final_sorted.bam.bai │   │   ├── SRR453566_sorted_dedup.txt │   │   ├── filtered.bam │   │   └── sorted_dedup.bam │   ├── qc │   │   ├── SRR453566.flagstat │   │   ├── SRR453566.insert_size_histogram.pdf -> /home/fchen3357/nf_work/14/eff8a139e40fb42296594a50bdce07/SRR453566.insert_size_histogram.pdf │   │   ├── SRR453566.insert_size_metrics.txt -> /home/fchen3357/nf_work/14/eff8a139e40fb42296594a50bdce07/SRR453566.insert_size_metrics.txt │   │   └── SRR453566.stats │   └── quant │   ├── SRR453566_featurecounts.txt │   └── SRR453566_featurecounts.txt.summary └── multiqc ├── alignment │   ├── multiqc_data │   │   ├── llms-full.txt │   │   ├── multiqc.log │   │   ├── multiqc.parquet │   │   ├── multiqc_citations.txt │   │   ├── multiqc_data.json │   │   ├── multiqc_general_stats.txt │   │   ├── multiqc_picard_dups.txt │   │   ├── multiqc_picard_insertSize.txt │   │   ├── multiqc_samtools_flagstat.txt │   │   ├── multiqc_samtools_stats.txt │   │   ├── multiqc_software_versions.txt │   │   ├── multiqc_sources.txt │   │   ├── multiqc_star.txt │   │   ├── picard_MarkIlluminaAdapters_histogram.txt │   │   ├── picard_MeanQualityByCycle_histogram.txt │   │   ├── picard_MeanQualityByCycle_histogram_1.txt │   │   ├── picard_QualityScoreDistribution_histogram.txt │   │   ├── picard_deduplication.txt │   │   ├── picard_insert_size_Counts.txt │   │   ├── picard_insert_size_Percentages.txt │   │   ├── samtools-flagstat-pct-table.txt │   │   ├── samtools-flagstat-table.txt │   │   ├── samtools-stats-dp.txt │   │   ├── samtools_alignment_plot.txt │   │   ├── star_alignment_plot.txt │   │   └── star_summary_table.txt │   └── multiqc_report.html └── read ├── multiqc_data │   ├── fastp-insert-size-plot.txt │   ├── fastp-seq-content-gc-plot_Read_1_After_filtering.txt │   ├── fastp-seq-content-gc-plot_Read_1_Before_filtering.txt │   ├── fastp-seq-content-gc-plot_Read_2_After_filtering.txt │   ├── fastp-seq-content-gc-plot_Read_2_Before_filtering.txt │   ├── fastp-seq-content-n-plot_Read_1_After_filtering.txt │   ├── fastp-seq-content-n-plot_Read_1_Before_filtering.txt │   ├── fastp-seq-content-n-plot_Read_2_After_filtering.txt │   ├── fastp-seq-content-n-plot_Read_2_Before_filtering.txt │   ├── fastp-seq-quality-plot_Read_1_After_filtering.txt │   ├── fastp-seq-quality-plot_Read_1_Before_filtering.txt │   ├── fastp-seq-quality-plot_Read_2_After_filtering.txt │   ├── fastp-seq-quality-plot_Read_2_Before_filtering.txt │   ├── fastp_filtered_reads_plot.txt │   ├── fastqc-status-check-heatmap.txt │   ├── fastqc_adapter_content_plot.txt │   ├── fastqc_per_base_n_content_plot.txt │   ├── fastqc_per_base_sequence_quality_plot.txt │   ├── fastqc_per_sequence_gc_content_plot_Counts.txt │   ├── fastqc_per_sequence_gc_content_plot_Percentages.txt │   ├── fastqc_per_sequence_quality_scores_plot.txt │   ├── fastqc_sequence_counts_plot.txt │   ├── fastqc_sequence_duplication_levels_plot.txt │   ├── fastqc_sequence_length_distribution_plot.txt │   ├── fastqc_top_overrepresented_sequences_table.txt │   ├── llms-full.txt │   ├── multiqc.log │   ├── multiqc.parquet │   ├── multiqc_citations.txt │   ├── multiqc_data.json │   ├── multiqc_fastp.txt │   ├── multiqc_fastqc.txt │   ├── multiqc_general_stats.txt │   ├── multiqc_software_versions.txt │   └── multiqc_sources.txt └── multiqc_report.html 28 directories, 186 files These outputs were generated from real sequencing datasets processed through the pipeline using publicly available NCBI SRA data, including SRR453566 (RNA-seq) and SRR27410792 (ATAC-seq).