V-pipe 1.0

• Downgrade LoFreq version to 2.1.3 due to a reported issue (CSB5/lofreq#89) and build the reference sequence index as a separate rule
• To build consensus sequences, report ambiguous base (N) when coverage is below 2 reads
• Generalize module to detect flow-cell cross-contamimation
• Basic report on number of reads after QC and alignment
• Allow to call SNVs with respect to a reference sequence, instead of the consensus sequences built from all data sets analysed within a single run of the pipeline