diff --git a/bolt/workflows/other/cancer_report.py b/bolt/workflows/other/cancer_report.py index 0799cd1..81e17fb 100644 --- a/bolt/workflows/other/cancer_report.py +++ b/bolt/workflows/other/cancer_report.py @@ -28,6 +28,10 @@ @click.option('--purple_dir', required=True, type=click.Path(exists=True)) @click.option('--virusbreakend_dir', required=True, type=click.Path(exists=True)) +@click.option('--mutpat_dir', required=True, type=click.Path(exists=True)) + +@click.option('--hrdetect_file', required=True, type=click.Path(exists=True)) +@click.option('--chord_file', required=True, type=click.Path(exists=True)) @click.option('--dragen_hrd_fp', required=True, type=click.Path(exists=True)) @@ -94,6 +98,10 @@ def entry(ctx, **kwargs): --key_genes {kwargs['cancer_genes_fp']} \ --oncokb_genes {kwargs['oncokb_genes_fp']} \ \ + --mutpat_dir {kwargs['mutpat_dir']} \ + --hrdetect_file {kwargs['hrdetect_file']} \ + --chord_file {kwargs['chord_file']} \ + \ --img_dir {output_image_dir}/ \ --result_outdir {output_table_dir}/ \ --out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html