diff --git a/.github/workflows/clinvar_runner.yaml b/.github/workflows/clinvar_runner.yaml index 94894a34..0ea377c4 100644 --- a/.github/workflows/clinvar_runner.yaml +++ b/.github/workflows/clinvar_runner.yaml @@ -32,5 +32,5 @@ jobs: curl --fail --silent --show-error -X POST \ -H "Authorization: Bearer $TOKEN" \ -H "Content-Type:application/json" \ - -d '{"output": "generate_clinvar_${{ steps.date.outputs.date }}", "dataset": "talos", "accessLevel": "full", "repo": "automated-interpretation-pipeline", "commit": "${{ github.sha }}", "cwd": "reanalysis", "script": ["./clinvar_runner.py"], "description": "Generate Latest Clinvar Summaries", "image": "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:1.1.5", "config": {"workflow": {"sequencing_type": "genome"}, "cohorts": {}}, "wait": false}' \ + -d '{"output": "generate_clinvar_${{ steps.date.outputs.date }}", "dataset": "talos", "accessLevel": "full", "repo": "automated-interpretation-pipeline", "commit": "${{ github.sha }}", "cwd": "reanalysis", "script": ["./clinvar_runner.py"], "description": "Generate Latest Clinvar Summaries", "image": "australia-southeast1-docker.pkg.dev/cpg-common/images/cpg_aip:1.1.5", "config": {"workflow": {"sequencing_type": "genome"}, "cohorts": {"talos": {"clinvar_filter": ["victorian clinical genetics services, murdoch childrens research institute"]}}}, "wait": false}' \ https://server-a2pko7ameq-ts.a.run.app diff --git a/helpers/prepare_aip_cohort.py b/helpers/prepare_aip_cohort.py index 989417fc..9b89b848 100644 --- a/helpers/prepare_aip_cohort.py +++ b/helpers/prepare_aip_cohort.py @@ -219,7 +219,9 @@ def process_pedigree( ped_lines = [] for entry in ped_with_permutations: for sample, mother, father in product( - entry['individual_id'], entry['paternal_id'], entry['maternal_id'] + entry['individual_id'], + entry['paternal_id'] or ['0'], + entry['maternal_id'] or ['0'], ): ped_lines.append( '\t'.join( diff --git a/reanalysis/clinvar_runner.py b/reanalysis/clinvar_runner.py index 829dc213..50d80c53 100644 --- a/reanalysis/clinvar_runner.py +++ b/reanalysis/clinvar_runner.py @@ -182,7 +182,7 @@ def main(date: str | None = None, folder: str | None = None): dependency = None - # generate a new round of clinva decisions + # generate a new round of clinvar decisions if not all(output.exists() for output in [clinvar_table_path, snv_vcf]): dependency = generate_clinvar_table(clinvar_table_path, folder, snv_vcf, date) diff --git a/reanalysis/summarise_clinvar_entries.py b/reanalysis/summarise_clinvar_entries.py index 9f608e94..db47b9a3 100644 --- a/reanalysis/summarise_clinvar_entries.py +++ b/reanalysis/summarise_clinvar_entries.py @@ -548,12 +548,13 @@ def main( all_decisions = sort_decisions(all_decisions) # if there's no defined config, write a local file + date_string = ( + date.strftime('%Y-%m-%d') if date else datetime.now().strftime('%Y-%m-%d') + ) try: - temp_output = output_path( - f'{date.strftime("%Y-%m-%d")}_clinvar_table.json', category='tmp' - ) + temp_output = output_path(f'{date_string}_clinvar_table.json', category='tmp') except (ConfigError, KeyError): - temp_output = f'{date.strftime("%Y-%m-%d")}_clinvar_table.json' + temp_output = f'{date_string}_clinvar_table.json' logging.info(f'temp JSON location: {temp_output}')