TRON-Bioinformatics/covigator-ngs-pipeline: v0.15.0

Changes Add support for input directly VCF (--vcf) files instead of FASTA or FASTQ files. These VCF files will be processed using the same normalization, phasing and annotation that we use for the full pipelines. If BAM files ((--bam and --bai)) are provided then the pipeline will also include technical annotations that allow to distinguish clonal from potential intrahost mutations. Add consensus FASTA derived from the VCF to the output folder. VCF normalization now runs before determining the consensus sequence for lineage determination. This has an effect on GATK Provide the reference file to mpileup right before call to ivar to reduce ivar calls as reported in #28 Phasing has been improved to avoid corner cases of merging overlapping indels Phasing is now more robust taking into account the FILTER value and the vafator_af annotation to merge mutations Bugfixes Python unit tests errors are now captured in the CI environment Phasing was wrongly skipped when using the default reference, this is now fixed Thanks to @Rohit-Satyam for his useful feedback