Nextflow ProteinFunction: support for SQLite db

[nakib103]

ENSVAR-6567

Extend ProteinFunction nextflow pipeline to be able to write to a SQLite db. It introduces the following params -

params.offline - if set, no ensembl database connection would be made (and not storing data in MySQL db)
params.sqlite - if set, a SQLite db would be created with the results. (if params.offline is set params.sqlite is automatically set too, otherwise there would be no output)
params.sqlite_dir - directory location where sqlite db should be stored. By default it is the param.outdir. The db name is set to ${params.species}_PolyPhen_SIFT.db
params.sqlite_db - give full path of the SQLite db with name. Alternative way to give db name.

Test:

nextflow run $ENSEMBL_ROOT_DIR/ensembl-variation/nextflow/ProteinFunction \
-profile $profile \
--sift_run_type FULL \
--outdir $PWD/temp \
--species felis_catus \
--offline 1 \
--gtf <gtf file>
--fasta <fasta file>

Test the generated SQLite db ($PWD/temp/felis_catus_PolyPhen_SIFT.db) against what we have in Ensembl database.