> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/nucleo-quality-control/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/nucleo-quality-control/interpretation-athena-coverage-report/installation-and-running.md).

# Installation and running

The athena tool is made of 3 parts; 1) annotate the bed file 2) generate statistic files 3) generate the coverage report. This can be run independently or together with a single workflow:

Run independently:

1. Annotate each region of the bed file with the gene, exon and per base coverage data using <https://github.com/msk-access/cwl-commandlinetools/blob/develop/athena/1.4.2/annotate_bed/annotate_bed.cwl>
2. Generate per exon and per gene statistics using <https://github.com/msk-access/cwl-commandlinetools/blob/develop/athena/1.4.2/coverage_stats_single/coverage_stats_single.cwl>
3. Generate HTML coverage report with <https://github.com/msk-access/cwl-commandlinetools/tree/develop/athena/1.4.2/coverage_report_single>

Run three steps with a single workflow:

* Run all 3 steps above using a single workflow using <https://github.com/msk-access/cwl_subworkflows/blob/develop/athena_report/athena_report.cwl>