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Merge branch 'main' into latest_report_only
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MattWellie authored Aug 28, 2023
2 parents 2faba06 + c21ac60 commit e90291f
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Showing 4 changed files with 10 additions and 7 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/clinvar_runner.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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
4 changes: 3 additions & 1 deletion helpers/prepare_aip_cohort.py
Original file line number Diff line number Diff line change
Expand Up @@ -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(
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2 changes: 1 addition & 1 deletion reanalysis/clinvar_runner.py
Original file line number Diff line number Diff line change
Expand Up @@ -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)

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9 changes: 5 additions & 4 deletions reanalysis/summarise_clinvar_entries.py
Original file line number Diff line number Diff line change
Expand Up @@ -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}')

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