v0.18.1

What's Changed

• Restored conda compatibility with newer nextflow versions by @johausmann in #53
• Implemented a pipeline mode to perform only the steps for lineage determination or genome generation @johausmann in #54
• Added mamba support and update pangolin lineage determination by @johausmann in #61

Full Changelog: v0.18.0...v0.18.1

v0.18.0

Changes

In order to support other viruses, this release brings a subworkflow to automatically create the snpEff database and bwa-mem 2 index from a custom annotation and genome

v0.17.0

Changes

• Fixes #26 and #41 by annotating VCFs with homoplasmic problematic sites from DeMaio. These are annotated in the field INFO/problematic. Also, all mutations at beginning and end of the genome are now filtered out.
• Changes the default VAFs to classify mutations and introduces a new classification. Low frequency are those below 2 % VAF, subclonal are above or equal 2 % and below 50 %, low quality clonal are above or equal 50 % and below 80 %; the rest are considered clonal.

v0.16.0

Changes

• Performance improvement by merging the last two steps (SnpEff and bgzip/tabix) into a single process

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!

v0.14.0

Changes

• Replace Picard mark duplicates by sambamba
• Remove unnecessary sort operation
• Limits memory used by SnpEff
• Replace BWA mem by BWA mem 2
• Add option to skip pangolin

Release v0.13.0

Changes

• Upgrade pangolin to v4.1.2

Release v0.12.0

Changes

• Drop references to GISAID

Release v0.11.0

Changes

• Replace the interpro domain names by pfam domain names for SARS-CoV-2 annotations. This is consistent with the data in the CoVigator database

Release v0.10.0

Changes

• Adds an optional step to trim primers when a bed with primer regions is provided with --primers. This is in particular to ARTIC protocol on Illumina.