Nextflow: Accept and split non-VCF input formats

[nuno-agostinho]

This PR improves the Nextlow pipeline to run VEP on non-VCF files.

Changelog

• Replace argument --vcf with --input
  • 8d2b87c50: --vcf still supported for backwards compatibility (now prints deprecated message)
• When giving (a folder with) input data to run VEP on:
  • Ignore files with specific extensions: ini, registry, tbi, csi
  • If vcf or vcf.gz extension, parse using checkVCF, generateSplits and splitVCF (as previously) before running VEP
  • If any other extensions, split input files with splitText based on params.bin_size before running VEP
• In the end, merge split files (as previously)
• 37e4e5b2f: New option --sort to sort VCF input/output from VEP (disabled by default)
• 388339075: Remove mentions to deprecated --skip_check
• Update documentation

Testing

Running the pipeline with different input files (input.tar.gz):

nextflow run ${ENSEMBL_ROOT_DIR}/ensembl-vep/nextflow/workflows/run_vep.nf \
  -profile slurm \
  -resume \
  --input input \
  --outdir outdir \
  --vep_config vep_config.ini