Updated output readme

![Python reporting - aligned fragments within peaks](images/py_frags_in_peaks.png)

### BEDtools

### Bedtools

<details markdown="1">

<summary>Output files</summary>

<details markdown="1">

<summary>Output files</summary>

- `reports/`

- `04_reporting/qc/`

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

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

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

<details markdown="1">

<summary>Output files</summary>

- `multiqc/`

- `04_reporting/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 markdown="1">

<summary>Output files</summary>

- `igv/`

- `04_reporting/igv/`

    - `igv_session.xml`: IGV session.

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

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<summary>Output files</summary>

- `deeptools/heatmaps/`

- `04_reporting/heatmaps/<gene/peak>/`

    - `.plotHeatmap.pdf`: heatmap PDF.

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

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

<details markdown="1">

<summary>Output files</summary>

- `genome/`

- `00_genome/target/`

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

- `genome/index/`

- `00_genome/target/index/`

    - `bowtie2`: Directory containing target Bowtie2 indices.

- `genome/spikein_index/`

- `00_genome/spikein/index/`

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

</details>

A number of genome-specific files are generated by the pipeline because they are required for the downstream processing of the results. If the `--save_reference` parameter is provided then these will be saved in the `genome/` directory. It is recommended to use the `--save_reference` parameter if you are using the pipeline to build new indices so that you can save them somewhere locally. The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space.

A number of genome-specific files are generated by the pipeline because they are required for the downstream processing of the results. If the `--save_reference` parameter is provided then these will be saved in the `00_genome/` directory. It is recommended to use the `--save_reference` parameter if you are using the pipeline to build new indices so that you can save them somewhere locally. The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space.

### Pipeline information