nf-100GMX-variant-summarizer v1

Nextflow pipeline used to count variants for the 100GMX project 'nf-100GMX-variant-summarizer' is a pipeline tool that counts variants in a VEPextended annotated VCF file. This pipeline generates 3 outputs: 1) a TSV file with the total number of SNV and indels 2) a TSV file with per sample counts for variants of type SNV, indel, novel, worldwide singletons, clinvar, gwascat and pharmgkb 3) a PDF file with the number of discernible variants in sample groups of interest. Important note: input file must be previously annotated by https://github.com/Iaguilaror/nf-VEPextended