Release 0.9.3

Changes

• BAM preprocessing is using a local folder as temp folder
• Pangolin is only executed for LoFreq and for the assembly results
• Pangolin now uses the provided CPUs
• Pangolin uses a local temp folder

Release v0.9.2

Bugfix

• Fix crash when phasing an empty VCF

Release v0.9.1

Bugfix

• Avoid issue with corrupted repository after first use when using the pipeline from github eg: nextflow run tron-bioinformatics/covigator-ngs-pipeline -r v0.9.0

Release v0.9.0

Changes

• Added a custom step phasing of clonal mutations. All clonal mutations (ie: clonal/not clonal determined by VAF) on the same amino acid are merged into a single mutation. This is not a read-backed phasing implementation which would allow to also phase intrahost mutations.
• Removed vt for decomposing complex mutations as the dependency was causing difficult to diagnose troubles in conda environments and it has virtually no impact in the output
• Improved documentation

Release v0.8.0

Changes

• Integrate pangolin for lineage determination.
• Integrate VAFator to annotate mutations with Variant Allele Frequency and subsequently classify them into clonal, intrahost or low frequency mutations.
• Remove unnecessary --chromosome parameter, this is now inferred from the reference.
• Transform iVar output table into VCF format and postprocess it similarly to other VCFs.
• Conda dependencies are now modular which minimises collisions of dependencies.
• Improve automated tests.
• Support for other virus than SARS-CoV-2 is now tested!

Release v0.7.0

Changes:

• Added parameters --input_fastas and --input_fastqs to enable the processing of multiple samples
• The code has been migrated to Nextflow DSL2 and organized into more readable modules

Bugfix:

• Domain annotations had the wrong coordinates and hence were wrong. These are fixed now

Release v0.6.0

Minor changes:

• The output folder is used as provided, no subfolder with the sample name is created

Release v0.5.0

Major changes:

• Add coverage analysis for FASTQ pipeline
• Add Pfam domain annotations in the output VCFs
• Add ConsHMM conservation scores annotations in the output VCFs

Minor changes:

• Parametrise chromosome for FASTA pipeline, default is the Sars-CoV-2 chromosome
• Parametrise global alignment parameters
• Avoid calling external Nextflow workflows and reimplement internally due to performance reasons. Logic does not change

Release Covigator NGS pipeline v0.4.0

Major changes

• Support DNA assemblies in FASTA format as input instead of raw reads. Variant calling on the assembly is implemented using BioPython PairwiseAligner and a valid VCF is created. This VCF is then normalized and annotated with SnpEff. Thus providing a VCF compatible with the VCFs generated from the FASTQ files.
• The variant normalization is reimplemented locally to avoid a call to Nextflow which was not efficient.

Minor changes

• Ensure the work folder are cleaned up after correct execution
• Add an initialization mode convenient to install the pipeline and initialize the conda environments before running on multiple samples concurrently.

Release Covigator NGS pipeline v0.3.1

Bugfix release

• The variant normalization workflow cached in the assets folder was sometimes causing an error when accessed concurrently. Although this is still the default behavior and it will just work in most cases, the tronflow dependencies can now be manually cloned and parametrized as a workaround for this issue.