Updated output

<details markdown="1">

<summary>Output files</summary>

* `01_prealign/merged_fastq/`

    * `*.merged.fastq.gz`: If `--save_merged_fastq` is specified, concatenated FastQ files will be placed in this directory.

- `01_prealign/merged_fastq/`

    - `*.merged.fastq.gz`: If `--save_merged_fastq` is specified, concatenated FastQ files will be placed in this directory.

</details>

<details markdown="1">

<summary>Output files</summary>

* `01_prealign/pretrim_fastqc/`

    * `*_fastqc.html`: FastQC report containing quality metrics.

    * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.

- `01_prealign/pretrim_fastqc/`

    - `*_fastqc.html`: FastQC report containing quality metrics.

    - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.

> **NB:** The FastQC plots in this directory are generated relative to the raw, input reads. They may contain adapter sequence and regions of low quality. To see how your reads look after adapter and quality trimming please refer to the FastQC reports in the `01_prealign/trimgalore/fastqc/` directory.

<details markdown="1">

<summary>Output files</summary>

* `01_prealign/trimgalore/`

    * `*.fq.gz`: If `--save_trimmed` is specified, FastQ files **after** adapter trimming will be placed in this directory.

    * `*_trimming_report.txt`: Log file generated by Trim Galore!.

* `01_prealign/trimgalore/fastqc/`

    * `*_fastqc.html`: FastQC report containing quality metrics for read 1 (*and read2 if paired-end*) **after** adapter trimming.

    * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.

- `01_prealign/trimgalore/`

    - `*.fq.gz`: If `--save_trimmed` is specified, FastQ files **after** adapter trimming will be placed in this directory.

    - `*_trimming_report.txt`: Log file generated by Trim Galore!.

- `01_prealign/trimgalore/fastqc/`

    - `*_fastqc.html`: FastQC report containing quality metrics for read 1 (*and read2 if paired-end*) **after** adapter trimming.

    - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.

</details>

<details markdown="1">

<summary>Output files</summary>

* `02_alignment/bowtie2`

- `02_alignment/bowtie2`

</details>

<details markdown="1">

<summary>Output files</summary>

* `aligner/bowtie2/intermediate/`

    * `.filtered.bam`: If `--publish_align_intermeds` is specified the original BAM file containing read alignments to the target genome will be placed in this directory.

    * `.filtered.bam.bai`: BAI file for BAM.

* `aligner/bowtie2/intermediate/samtools_stats`

    * `.filtered.bam.*stats`: various statistics regarding the BAM files.

- `aligner/bowtie2/intermediate/`

    - `.filtered.bam`: If `--publish_align_intermeds` is specified the original BAM file containing read alignments to the target genome will be placed in this directory.

    - `.filtered.bam.bai`: BAI file for BAM.

- `aligner/bowtie2/intermediate/samtools_stats`

    - `.filtered.bam.*stats`: various statistics regarding the BAM files.

</details>

<details markdown="1">

<summary>Output files</summary>

* `02_alignment/bowtie2/target/markdup/`

    * `.markdup.bam`: Coordinate sorted BAM file after duplicate marking. This is the final post-processed BAM file and so will be saved by default in the results directory.

    * `.markdup.bam.bai`: BAI index file for coordinate sorted BAM file after duplicate marking. This is the final post-processed BAM index file and so will be saved by default in the results directory.

* `02_alignment/bowtie2/target/markdup/picard_metrics`

    * `.markdup.MarkDuplicates.metrics.txt`: Metrics file from MarkDuplicates.

- `02_alignment/bowtie2/target/markdup/`

    - `.markdup.bam`: Coordinate sorted BAM file after duplicate marking. This is the final post-processed BAM file and so will be saved by default in the results directory.

    - `.markdup.bam.bai`: BAI index file for coordinate sorted BAM file after duplicate marking. This is the final post-processed BAM index file and so will be saved by default in the results directory.

- `02_alignment/bowtie2/target/markdup/picard_metrics`

    - `.markdup.MarkDuplicates.metrics.txt`: Metrics file from MarkDuplicates.

</details>

<details markdown="1">

<summary>Output files</summary>

* `03_peak_calling/01_bam_to_bedgraph`

    * `*.bedgraph`: bedgraph coverage file.

- `03_peak_calling/01_bam_to_bedgraph`

    - `*.bedgraph`: bedgraph coverage file.

</details>

<details markdown="1">

<summary>Output files</summary>

* `03_peak_calling/03_bed_to_bigwig`

    * `*.bigWig`: bigWig coverage file.

- `03_peak_calling/03_bed_to_bigwig`

    - `*.bigWig`: bigWig coverage file.

</details>

<details markdown="1">

<summary>Output files</summary>

* `03_peak_calling/04_called_peaks/`

    * `.peaks*.bed`: BED file containing peak coordinates and peak signal.

- `03_peak_calling/04_called_peaks/`

    - `.peaks*.bed`: BED file containing peak coordinates and peak signal.

</details>

<details markdown="1">

<summary>Output files</summary>

* `seacr/`

    * `{group}.consensus_peaks.pdf`: schematic showing which consensus peaks are shared across replicates within groups

    * `all_peaks.consensus_peaks.pdf`: schematic showing which consensus peaks are shared across all samples

* `seacr/consensus_peaks`

    * `{group}.consensus.peaks.bed`: BED containing consensus peaks for each group

    * `all_peaks.consensus.peaks.bed`: BED containing consensus peaks across all samples

- `seacr/`

    - `{group}.consensus_peaks.pdf`: schematic showing which consensus peaks are shared across replicates within groups

    - `all_peaks.consensus_peaks.pdf`: schematic showing which consensus peaks are shared across all samples

- `seacr/consensus_peaks`

    - `{group}.consensus.peaks.bed`: BED containing consensus peaks for each group

    - `all_peaks.consensus.peaks.bed`: BED containing consensus peaks across all samples

</details>

<details markdown="1">

<summary>Output files</summary>

* `reports/`

    * `report.pdf`: PDF report of all plots.

    * `*.png`: individual plots featured in the PDF report.

    * `*.csv`: corresponding data used to produce the plot.

- `reports/`

    - `report.pdf`: PDF report of all plots.

    - `*.png`: individual plots featured in the PDF report.

    - `*.csv`: corresponding data used to produce the plot.

</details>

<details markdown="1">

<summary>Output files</summary>

* `multiqc/`

    * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.

    * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.

    * `multiqc_plots/`: directory containing static images from the report in various formats.

- `multiqc/`

    - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.

    - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.

    - `multiqc_plots/`: directory containing static images from the report in various formats.

</details>

### IGV

<details markdown="1">

<summary>Output files</summary>

* `igv/`

    * `igv_session.xml`: IGV session.

    * `*.txt`: IGV input file configurations.

- `igv/`

    - `igv_session.xml`: IGV session.

    - `*.txt`: IGV input file configurations.

</details>

<details markdown="1">

<summary>Output files</summary>

* `deeptools/heatmaps/`

    * `.plotHeatmap.pdf`: heatmap PDF.

    * `.computeMatrix.mat.gz`: heatmap matrix.

    * `*.mat.tab`: matrix and heatmap configs.

- `deeptools/heatmaps/`

    - `.plotHeatmap.pdf`: heatmap PDF.

    - `.computeMatrix.mat.gz`: heatmap matrix.

    - `*.mat.tab`: matrix and heatmap configs.

</details>

<details markdown="1">

<summary>Output files</summary>

* `genome/`

    * `*.fa`: If the `--save_reference` parameter is provided then all of the genome reference files will be placed in this directory.

* `genome/index/`

    * `bowtie2`: Directory containing target Bowtie2 indices.

* `genome/spikein_index/`

    * `bowtie2`: Directory containing spike-in Bowtie2 indices.

- `genome/`

    - `*.fa`: If the `--save_reference` parameter is provided then all of the genome reference files will be placed in this directory.

- `genome/index/`

    - `bowtie2`: Directory containing target Bowtie2 indices.

- `genome/spikein_index/`

    - `bowtie2`: Directory containing spike-in Bowtie2 indices.

</details>

<details markdown="1">

<summary>Output files</summary>

* `pipeline_info/`

    * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.

    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.csv`.

    * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.

- `pipeline_info/`

    - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.

    - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.csv`.

    - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.

</details>