Nextflow VEP: support Seqera platform - Githubissues

Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

https://www.ensembl.org/vep

Apache License 2.0

456 stars 152 forks source link

Nextflow VEP: support Seqera platform #1724

Closed nuno-agostinho closed 3 months ago

nuno-agostinho commented 4 months ago

ENSVAR-5853: Changes to organisation of Nextflow VEP files in order to support Seqera platform

Changelog

Accept headerless VCF files
- If a VCF has no header, process as a normal text file (like done for non-VCF input files)
Add main.nf and nextflow.config to root directory
Move nextflow.config to nextflow directory
Rename the nf-modules directory to modules
Add Nextflow schema
- Move pipeline parameters to nextflow.config
- Add sections of nf-core config template to nextflow.config
Updated README.md

Testing

Run pipeline using:

nextflow run nuno-agostinho/ensembl-vep -r nextflow/seqera-platform

After the pipeline is merged to main and release branches, it can be run properly:

nextflow run Ensembl/ensembl-vep
nextflow run Ensembl/ensembl-vep -r release/113