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:
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
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
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
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