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
Changes Add support for input directly VCF (--vcf) files instead of FASTA or FASTQ files. These VCF...
Changes It creates the reference genome indices if not available Bugfix The SplitNCigarReads oper...
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
First pre-release integrating alignment, mark duplicates, realignment around indels, variant calling...
Bugfix Avoid issue with corrupted repository after first use when using the pipeline from github eg...
A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annota...
Major changes Support DNA assemblies in FASTA format as input instead of raw reads. Variant calli...
Major changes Add read trimming with fastp Output QC results in JSON format Integrate 4 variant...
Major changes: Add coverage analysis for FASTQ pipeline Add Pfam domain annotations in the outpu...
Changes Performance improvement by merging the last two steps (SnpEff and bgzip/tabix) into a singl...
Changes BAM preprocessing is using a local folder as temp folder Pangolin is only executed for LoFr...
Changes Added a custom step phasing of clonal mutations. All clonal mutations (ie: clonal/not clona...
Bugfix Python dependencies are defined now in a more flexible way using the compatibility operator ...
Changes Integrate pangolin for lineage determination. Integrate VAFator to annotate mutations with ...
Bugfixes: Library distributed version was not specified and it was causing some incompatibility wit...
Changes Add support for input directly VCF (--vcf) files instead of FASTA or FASTQ files. These VCF...
Changes It creates the reference genome indices if not available Bugfix The SplitNCigarReads oper...
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
First pre-release integrating alignment, mark duplicates, realignment around indels, variant calling...
Bugfix Avoid issue with corrupted repository after first use when using the pipeline from github eg...
A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annota...
Major changes Support DNA assemblies in FASTA format as input instead of raw reads. Variant calli...
Major changes Add read trimming with fastp Output QC results in JSON format Integrate 4 variant...
Major changes: Add coverage analysis for FASTQ pipeline Add Pfam domain annotations in the outpu...
Changes Performance improvement by merging the last two steps (SnpEff and bgzip/tabix) into a singl...
Changes BAM preprocessing is using a local folder as temp folder Pangolin is only executed for LoFr...
Changes Added a custom step phasing of clonal mutations. All clonal mutations (ie: clonal/not clona...
Bugfix Python dependencies are defined now in a more flexible way using the compatibility operator ...
Changes Integrate pangolin for lineage determination. Integrate VAFator to annotate mutations with ...
Bugfixes: Library distributed version was not specified and it was causing some incompatibility wit...
Changes Add support for input directly VCF (--vcf) files instead of FASTA or FASTQ files. These VCF...
Changes It creates the reference genome indices if not available Bugfix The SplitNCigarReads oper...
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
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