feat(pipeline): VEP database mode, and a pipeline-specific database URL
Makes a real annotation runnable locally without the 25 GB VEP cache, which is what the demo needs and what a reviewer can reproduce in minutes. - params.vep_database (VEP_DATABASE=true) queries Ensembl's public database instead of a local cache. Slower per variant and fewer fields, so --everything is swapped for the flags the loader actually stores. Its cache placeholder is NO_CACHE, not NO_FILE: Nextflow rejects two staged inputs sharing a filename. - PIPELINE_DATABASE_URL is handed to the pipeline when set. The loader runs inside a container, where the API's own localhost URL would point at the container itself. - README: how to run the UI's annotate button locally against host Nextflow + Docker. Verified end to end on pipeline/tests/data/tiny.vcf: bcftools norm split the multiallelic record, VEP 113 annotated 4 variants live, the loader wrote them and marked the job succeeded, and the UI shows them. The deletion came back as 22:42126611 CT>C with exact VCF alleles, which is the case the audit's ID-tagging fix exists for. Tests: api 51, loader 16, stub run 3/3; ruff, mypy clean.
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@@ -14,7 +14,10 @@ workflow {
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def must_exist = !workflow.stubRun
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vcf_ch = Channel.fromPath(params.vcf, checkIfExists: true)
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cache = file(params.vep_cache, checkIfExists: must_exist)
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// In database mode there is no cache to stage. Its placeholder differs from the plugin one:
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// Nextflow rejects two staged inputs that share a filename.
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cache = file(params.vep_database ? "${projectDir}/assets/NO_CACHE" : params.vep_cache,
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checkIfExists: must_exist && !params.vep_database)
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plugins = file(params.vep_plugin_data ?: "${projectDir}/assets/NO_FILE", checkIfExists: must_exist)
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NORMALISE(vcf_ch)
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