kemal
5463f489a3
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End-to-end variant interpretation platform for rare genetic disease research: SvelteKit UI, FastAPI + PostgreSQL API, Nextflow/Ensembl VEP pipeline, LightGBM pathogenicity scoring with MLflow, K8s/ArgoCD/GCP infrastructure. Public test data only; no clinical claims.
25 lines
822 B
Plaintext
25 lines
822 B
Plaintext
params {
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vcf = null
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job_id = null
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db_url = null
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outdir = "results"
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assembly = "GRCh38"
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vep_cache = "${projectDir}/cache/vep" // download once with `vep_install`; or use --offline false
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vep_plugins = "CADD,AlphaMissense"
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}
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profiles {
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docker { docker.enabled = true }
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gcp {
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process.executor = 'k8s' // runs inside GKE via Argo; Nextflow k8s executor
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workDir = "gs://${params.bucket}/work"
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google.project = params.project
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}
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}
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process {
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withName: VEP { container = 'ensemblorg/ensembl-vep:release_113.0'; cpus = 4; memory = '8 GB' }
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withName: NORMALISE { container = 'quay.io/biocontainers/bcftools:1.20--h8b25389_0' }
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withName: LOAD_DB { container = 'ghcr.io/lynchaos/rarelens-loader:latest' }
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}
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