Kemal Yaylali
11fb6b3d73
An end-to-end audit found the repo could not build, test or run as shipped. This fixes every finding, then adds a Cloud Run track so the demo costs about £1/month idle instead of ~£150. CI (red on its first run) - api: setuptools could not build the package (flat layout with app/ and alembic/) - web: missing @types/node; `vitest run` exited 1 with no test files - pipeline: the stub run needed a gitignored VCF, and no process had a stub block - ruff pinned, mypy configured, DB tests on real Postgres (pgserver locally, service in CI) ML serving (scores were meaningless) - the registered model now carries its own feature engineering and returns predict_proba, so serving sends raw columns and cannot drift from training - resolve by registry alias (stages are deprecated in MLflow 3) and record the real version; re-scoring upserts instead of failing on the unique constraint - ClinVar labels parsed from VEP's lowercase terms Pipeline - exact ref/alt recovered from a CHROM_POS_REF_ALT VCF ID; loading is idempotent - job status reaches running/failed/succeeded, so the UI stops polling dead jobs - DATABASE_URL travels in the environment or a Nextflow secret, never on a command line - VEP cache and plugins staged as inputs; the gcp profile runs tasks on Google Batch Deployment - the API serves /api (matching the ingress); the web app reads its API URL at runtime - migrations run in an init container under a Postgres advisory lock - terraform: custom VPC shared with Batch, private Cloud SQL, API enablement, Workload Identity bindings, Secret Manager, deletion protection - serverless track, now the default: Cloud Run services scaling to zero, a Cloud Run job for the Nextflow driver, and Neon or Cloud SQL behind one DATABASE_URL secret. GKE and Argo remain, behind -var deploy_kubernetes=true. See docs/cloud.md. Correctness and security - 409 on duplicate sample names, 422 on bad paging, natural chromosome ordering, wider VEP text columns, enum dropped on downgrade, the sample's assembly actually used - vcf_uri restricted to gs:// objects or files under the data root, blocking option injection - CORS restricted to configured origins; `make down` no longer deletes volumes Data - docs/data.md records the peer-reviewed, openly licensed sources (GIAB HG002, ClinVar, gnomAD) with citations and an honest evaluation plan; `make data` fetches a chr22 slice Verified: api 50 tests, ml 18, loader 16, web 12; ruff, mypy, svelte-check, terraform validate and both kustomize overlays clean.
32 lines
1.2 KiB
Plaintext
32 lines
1.2 KiB
Plaintext
process VEP {
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tag "$vcf.simpleName"
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publishDir params.outdir, mode: 'copy'
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input:
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path vcf
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path cache // staged as an input so it is visible inside the container
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path plugin_data // assets/NO_FILE when plugins are not configured
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output:
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path "${vcf.simpleName}.vep.tsv", emit: tsv
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path "${vcf.simpleName}.vep_summary.html"
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script:
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// Plugins run only when --vep_plugin_data names a directory holding the plugin modules
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// (INSTALL.pl -a p -g CADD,AlphaMissense -r <dir>) and the data files named in params.
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def plugins = plugin_data.name == 'NO_FILE' ? '' : [
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"--dir_plugins ${plugin_data}",
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"--plugin CADD,snv=${plugin_data}/${params.cadd_snv},indels=${plugin_data}/${params.cadd_indels}",
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"--plugin AlphaMissense,file=${plugin_data}/${params.alphamissense}",
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].join(' ')
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"""
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vep -i $vcf -o ${vcf.simpleName}.vep.tsv --tab \\
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--assembly ${params.assembly} --cache --offline --dir_cache ${cache} \\
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--everything --pick ${plugins} \\
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--stats_file ${vcf.simpleName}.vep_summary.html --fork ${task.cpus}
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"""
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stub:
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"""
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touch ${vcf.simpleName}.vep.tsv ${vcf.simpleName}.vep_summary.html
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"""
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}
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