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.
17 lines
556 B
Plaintext
17 lines
556 B
Plaintext
process VEP {
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tag "$vcf.simpleName"
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publishDir params.outdir, mode: 'copy'
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input: path vcf
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output:
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path "${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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"""
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vep -i $vcf -o ${vcf.simpleName}.vep.tsv --tab \\
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--assembly ${params.assembly} --cache --dir_cache ${params.vep_cache} --offline \\
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--everything --pick --af_gnomade --plugin CADD --plugin AlphaMissense \\
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--stats_file ${vcf.simpleName}.vep_summary.html --fork ${task.cpus}
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"""
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}
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