diff --git a/bolt/workflows/other/cancer_report.py b/bolt/workflows/other/cancer_report.py index 0799cd1..983f596 100644 --- a/bolt/workflows/other/cancer_report.py +++ b/bolt/workflows/other/cancer_report.py @@ -29,7 +29,7 @@ @click.option('--purple_dir', required=True, type=click.Path(exists=True)) @click.option('--virusbreakend_dir', required=True, type=click.Path(exists=True)) -@click.option('--dragen_hrd_fp', required=True, type=click.Path(exists=True)) +@click.option('--dragen_hrd_fp', required=False, type=click.Path(exists=True)) @click.option('--cancer_genes_fp', required=True, type=click.Path(exists=True)) @click.option('--oncokb_genes_fp', required=True, type=click.Path(exists=True)) @@ -62,6 +62,11 @@ def entry(ctx, **kwargs): batch_name = f'{kwargs["subject_name"]}_{kwargs["tumor_name"]}' output_table_dir = output_dir / 'cancer_report_tables' + # Optional dragen hrd argument + dragen_hrd_arg = '' + if kwargs['dragen_hrd_fp']: + dragen_hrd_arg = f"--dragen_hrd {kwargs['dragen_hrd_fp']}" + # Run gpgr canrep command = fr''' gpgr.R canrep \ @@ -88,7 +93,7 @@ def entry(ctx, **kwargs): --virusbreakend_tsv {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf.summary.tsv \ --virusbreakend_vcf {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf \ \ - --dragen_hrd {kwargs['dragen_hrd_fp']} \ + {dragen_hrd_arg} \ --bcftools_stats {kwargs['smlv_somatic_bcftools_stats_fp']} \ \ --key_genes {kwargs['cancer_genes_fp']} \ @@ -96,7 +101,7 @@ def entry(ctx, **kwargs): \ --img_dir {output_image_dir}/ \ --result_outdir {output_table_dir}/ \ - --out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html + --out_file {output_dir}/{kwargs['tumor_name']}.cancer_report.html ''' util.execute_command(command)