@@ -237,7 +237,7 @@ Additional QC and analysis pertaining particularly to CUT&Run and CUT&Tag data a
[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarizing all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
> **NB:** The FastQC plots displayed in the MultiQC report shows **untrimmed** reads. They may contain adapter sequence and potentially regions with low quality.
<detailsmarkdown="1">
<summary>Output files</summary>
@@ -301,10 +301,10 @@ A number of genome-specific files are generated by the pipeline because they are
<detailsmarkdown="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.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
* 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.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
- Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
