Nextflow Modules
Showing module(s) with keyword "vep"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/custom/addmostsevereconsequence | Process | annotation vep consequence vcf | Annotate a VEP annotated VCF with the most severe consequence field |
| nf-core/custom/addmostseverepli | Process | annotation vep pli vcf | Annotate a VEP annotated VCF with the most severe pLi field |
| nf-core/vcf_annotate_vepyr | Workflow | vcf annotation normalisation vep vepyr bcftools huggingface | Optionally download a vepyr cache from Hugging Face and normalise a VCF with bcftools norm, then annotate it with Ensembl VEP consequences using vepyr and return the bgzip VCF with its tabix index. Give the cache either as `ch_cache` or as a Hugging Face dataset in `val_hf_repo`, such as `biodatageeks/vepyr_116_GRCh38_ensembl`; setting both, or neither, is an error. The repository is downloaded once and shared across all samples. To pin the cache or download only some contigs, add `--revision` and `--include` to `HUGGINGFACE_DOWNLOAD`'s `ext.args`. A partial download must include every entity's manifest and all contigs present in the VCF: ``` withName: 'HUGGINGFACE_DOWNLOAD' { ext.args = "--revision <commit> --include '*/chr22.parquet' --include '*/chrom_manifest.json'" } ``` What bcftools norm does comes from `BCFTOOLS_NORM`'s `ext.args`. Keep its output bgzip VCF (`--output-type z`): `VEPYR_ANNOTATE` runs a single pipeline for BCF (`-Ob`, `-Ou`) and plain VCF (`-Ov`). vepyr's Ensembl VEP parity tests use this configuration, which splits multiallelic records without left-aligning indels. `--write-index=tbi` is optional and saves the tabix step in `VEPYR_ANNOTATE`: ``` withName: 'BCFTOOLS_NORM' { ext.args = '--multiallelics -both --do-not-normalize --output-type z --write-index=tbi' } ``` |
| nf-core/vepyr/annotate | Process | annotation vcf variant vep | Annotate a VCF with Ensembl VEP consequences using vepyr, a Rust reimplementation of the Variant Effect Predictor. Annotation features are controlled through `task.ext.args`. |