Release of VLQ-nf using only GISAID for reference data reconstruction

• lose unused functionalities and parameter flags from development stages
• specifically: only allow GISAID input for reference data reconstruction

Initial Release of VLQ-nf

• Detect and quantify SARS-CoV-2 lineages from wastewater samples
• Nextflow workflow based on the wastewater_analysis pipeline by Baaijens, Zulli, Ott et al.
• Reconstruct reference db from GISAID data: mimic pandemic background and filter lineage-characteristic mutation profiles
• Repurpose Kallisto for lineage quantification based on pseudo-alignment of wastewater reads against a reference index