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nf-core/viralrecon: nf-core/viralrecon v2.0 - Silver Ferret

Harshil Patel; Sarai Varona; Sara Monzón; Jose Espinosa-Carrasco; Michael L Heuer; Gisela Gabernet; MiguelJulia; Phil Ewels; Stephen Kelly; Katrin Sameith; Maxime U. Garcia; jcurado

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<oai_dc:dc xmlns:dc="" xmlns:oai_dc="" xmlns:xsi="" xsi:schemaLocation="">
  <dc:creator>Harshil Patel</dc:creator>
  <dc:creator>Sarai Varona</dc:creator>
  <dc:creator>Sara Monzón</dc:creator>
  <dc:creator>Jose Espinosa-Carrasco</dc:creator>
  <dc:creator>Michael L Heuer</dc:creator>
  <dc:creator>Gisela Gabernet</dc:creator>
  <dc:creator>Phil Ewels</dc:creator>
  <dc:creator>Stephen Kelly</dc:creator>
  <dc:creator>Katrin Sameith</dc:creator>
  <dc:creator>Maxime U. Garcia</dc:creator>
  <dc:description>[2.0] - 2021-05-13
:warning: Major enhancements

Pipeline has been re-implemented in Nextflow DSL2
All software containers are now exclusively obtained from Biocontainers
Updated minimum Nextflow version to v21.04.0 (see nextflow#572)
BCFtools and iVar will be run by default for Illumina metagenomics and amplicon data, respectively. However, this behaviour can be customised with the --callers parameter.
Variant graph processes to call variants relative to the reference genome directly from de novo assemblies have been deprecated and removed
Variant calling with Varscan 2 has been deprecated and removed due to licensing restrictions
New tools:
Pangolin for lineage analysis
Nextclade for clade assignment, mutation calling and consensus sequence quality checks
ASCIIGenome for individual variant screenshots with annotation tracks

Other enhancements &amp; fixes

Illumina and Nanopore runs containing the same 48 samples sequenced on both platforms have been uploaded to the nf-core AWS account for full-sized tests on release
Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation
Default human --kraken2_db link has been changed from Zenodo to an AWS S3 bucket for more reliable downloads
Updated pipeline template to nf-core/tools 1.14
Optimise MultiQC configuration and input files for faster run-time on huge sample numbers
[#122] - Single SPAdes command to rule them all
[#138] - Problem masking the consensus sequence
[#142] - Unknown method invocation toBytes on String type
[#169] - ggplot2 error when generating mosdepth amplicon plot with Swift v2 primers
[#170] - ivar trimming of Swift libraries new offset feature
[#175] - MultiQC report does not include all the metrics
[#188] - Add and fix EditorConfig linting in entire pipeline


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  <dc:title>nf-core/viralrecon: nf-core/viralrecon v2.0 - Silver Ferret</dc:title>
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