nextflow-vep: separate out CLI params configuration

[nakib103]

nextflow-vep does not allow many-to-many scenario between input VCF and VEP config files. This PR allows for the case where we use nextflow-vep from another pipeline. This is achieved by separating out the processing of CLI params and allocating that jobs to main workflow (which is used when we call nextflow-vep from CLI).

It is the responsibility of the workflow that is calling nextflow-vep to pass the VCF file and related VEP config inside a tuple.

meta map: we also introduce meta map as input parameter to vep workflow -

tuple val(meta), path(vcf), path(vcf_index), path(vep_config)

It is useful to use it instead of long length of parameters list in the process input. Some of which are only passed through to be used by some other downstream process.

Test

You can create a test nextflow pipeline to test the new updates -

include { vep } from "${params.repo_dir}/ensembl-vep/nextflow/workflows/run_vep.nf"

workflow {
	meta = [:]
        meta.one_to_many = 0
        meta.index_type = "tabix"

       ch_vep = Channel.of( [meta, file("path.to.vcf.file"), file("path.to.vcf.file.inedx"), file("path.to.vep_config") ])
}

nextflow-vep should also be tested in CLI mode to see if one-to-one, one-to-many, and many-to-one scenario works.

[dbolser]

Has this been tested?

[nuno-agostinho]

Hey @nakib103, this PR seems to be working as intended!

All scenarios work when using the main workflow and also the sub-workflow works as expected. Thanks!

[nuno-agostinho]

Merged to main and release/112.