Kemal Yaylali
ae58e33fe2
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.
36 lines
1.6 KiB
Plaintext
36 lines
1.6 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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// --everything needs the cache (it implies --af_gnomade and friends); the database offers a
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// smaller set, but still the consequence, gene, HGVS and ClinVar fields the loader stores.
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def source = params.vep_database ? "--database" : "--cache --offline --dir_cache ${cache}"
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def fields = params.vep_database ? "--symbol --hgvs --canonical --biotype --variant_class --check_existing" : "--everything"
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"""
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vep -i $vcf -o ${vcf.simpleName}.vep.tsv --tab \\
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--assembly ${params.assembly} ${source} \\
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${fields} --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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