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.
16 lines
434 B
Plaintext
16 lines
434 B
Plaintext
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { NORMALISE } from './modules/normalise'
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include { VEP } from './modules/vep'
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include { LOAD_DB } from './modules/load_db'
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workflow {
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if (!params.vcf) error "Provide --vcf"
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vcf_ch = Channel.fromPath(params.vcf, checkIfExists: true)
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NORMALISE(vcf_ch)
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VEP(NORMALISE.out.vcf)
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LOAD_DB(VEP.out.tsv, params.job_id ?: 'local', params.db_url ?: 'none')
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}
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