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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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  <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>MiguelJulia</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:creator>jcurado</dc:creator>
  <dc:date>2021-05-13</dc:date>
  <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

Parameters


Old parameter
New parameter




--amplicon_bed
--primer_bed


--amplicon_fasta
--primer_fasta


--amplicon_left_suffix
--primer_left_suffix


--amplicon_right_suffix
--primer_right_suffix


--filter_dups
--filter_duplicates


--skip_adapter_trimming
--skip_fastp


--skip_amplicon_trimming
--skip_cutadapt



--artic_minion_aligner



--artic_minion_caller



--artic_minion_medaka_model



--asciigenome_read_depth



--asciigenome_window_size



--blast_db



--enable_conda



--fast5_dir



--fastq_dir



--ivar_trim_offset



--kraken2_assembly_host_filter



--kraken2_variants_host_filter



--min_barcode_reads



--min_guppyplex_reads



--multiqc_title



--platform



--primer_set



--primer_set_version



--public_data_ids



--save_trimmed_fail



--save_unaligned



--sequencing_summary



--singularity_pull_docker_container



--skip_asciigenome



--skip_bandage



--skip_consensus



--skip_ivar_trim



--skip_nanoplot



--skip_pangolin



--skip_pycoqc



--skip_nextclade



--skip_sra_fastq_download



--spades_hmm



--spades_mode


--cut_mean_quality



--filter_unmapped



--ivar_trim_min_len



--ivar_trim_min_qual



--ivar_trim_window_width



--kraken2_use_ftp



--max_allele_freq



--min_allele_freq



--min_base_qual



--min_coverage



--min_trim_length



--minia_kmer



--mpileup_depth



--name



--qualified_quality_phred



--save_align_intermeds



--save_kraken2_fastq



--save_sra_fastq



--skip_sra



--skip_vg



--unqualified_percent_limit



--varscan2_strand_filter



NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.
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  <dc:identifier>https://zenodo.org/record/4757535</dc:identifier>
  <dc:identifier>10.5281/zenodo.4757535</dc:identifier>
  <dc:identifier>oai:zenodo.org:4757535</dc:identifier>
  <dc:relation>url:https://github.com/nf-core/viralrecon/tree/2.0</dc:relation>
  <dc:relation>doi:10.5281/zenodo.3901628</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/covid-19</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/zenodo</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:title>nf-core/viralrecon: nf-core/viralrecon v2.0 - Silver Ferret</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
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