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