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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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  <identifier identifierType="DOI">10.5281/zenodo.4757535</identifier>
  <creators>
    <creator>
      <creatorName>Harshil Patel</creatorName>
      <affiliation>The Francis Crick Institute</affiliation>
    </creator>
    <creator>
      <creatorName>Sarai Varona</creatorName>
    </creator>
    <creator>
      <creatorName>Sara Monzón</creatorName>
      <affiliation>BU-ISCIII</affiliation>
    </creator>
    <creator>
      <creatorName>Jose Espinosa-Carrasco</creatorName>
    </creator>
    <creator>
      <creatorName>Michael L Heuer</creatorName>
      <affiliation>UC Berkeley AMPLab/RISE Lab</affiliation>
    </creator>
    <creator>
      <creatorName>Gisela Gabernet</creatorName>
      <affiliation>@qbicsoftware</affiliation>
    </creator>
    <creator>
      <creatorName>MiguelJulia</creatorName>
    </creator>
    <creator>
      <creatorName>Phil Ewels</creatorName>
      <affiliation>Science for Life Laboratory</affiliation>
    </creator>
    <creator>
      <creatorName>Stephen Kelly</creatorName>
    </creator>
    <creator>
      <creatorName>Katrin Sameith</creatorName>
      <affiliation>DRESDEN-concept Genome Center</affiliation>
    </creator>
    <creator>
      <creatorName>Maxime U. Garcia</creatorName>
      <affiliation>@SciLifeLab | Karolinska Institutet</affiliation>
    </creator>
    <creator>
      <creatorName>jcurado</creatorName>
      <affiliation>@Flomics</affiliation>
    </creator>
  </creators>
  <titles>
    <title>nf-core/viralrecon: nf-core/viralrecon v2.0 - Silver Ferret</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <dates>
    <date dateType="Issued">2021-05-13</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4757535</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/nf-core/viralrecon/tree/2.0</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3901628</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/covid-19</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <version>2.0</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">[&lt;a href="https://github.com/nf-core/rnaseq/releases/tag/2.0"&gt;2.0&lt;/a&gt;] - 2021-05-13
:warning: Major enhancements
&lt;ul&gt;
&lt;li&gt;Pipeline has been re-implemented in &lt;a href="https://www.nextflow.io/docs/latest/dsl2.html"&gt;Nextflow DSL2&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;All software containers are now exclusively obtained from &lt;a href="https://biocontainers.pro/#/registry"&gt;Biocontainers&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;Updated minimum Nextflow version to &lt;code&gt;v21.04.0&lt;/code&gt; (see &lt;a href="https://github.com/nextflow-io/nextflow/issues/1964"&gt;nextflow#572&lt;/a&gt;)&lt;/li&gt;
&lt;li&gt;&lt;a href="http://samtools.github.io/bcftools/bcftools.html"&gt;BCFtools&lt;/a&gt; and &lt;a href="https://github.com/andersen-lab/ivar"&gt;iVar&lt;/a&gt; will be run by default for Illumina metagenomics and amplicon data, respectively. However, this behaviour can be customised with the &lt;code&gt;--callers&lt;/code&gt; parameter.&lt;/li&gt;
&lt;li&gt;Variant graph processes to call variants relative to the reference genome directly from &lt;em&gt;de novo&lt;/em&gt; assemblies have been deprecated and removed&lt;/li&gt;
&lt;li&gt;Variant calling with Varscan 2 has been deprecated and removed due to &lt;a href="https://github.com/dkoboldt/varscan/issues/12"&gt;licensing restrictions&lt;/a&gt;&lt;/li&gt;
&lt;li&gt;New tools:&lt;ul&gt;
&lt;li&gt;&lt;a href="https://github.com/cov-lineages/pangolin"&gt;Pangolin&lt;/a&gt; for lineage analysis&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nextstrain/nextclade"&gt;Nextclade&lt;/a&gt; for clade assignment, mutation calling and consensus sequence quality checks&lt;/li&gt;
&lt;li&gt;&lt;a href="https://asciigenome.readthedocs.io/en/latest/"&gt;ASCIIGenome&lt;/a&gt; for individual variant screenshots with annotation tracks&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;/ul&gt;
Other enhancements &amp;amp; fixes
&lt;ul&gt;
&lt;li&gt;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&lt;/li&gt;
&lt;li&gt;Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation&lt;/li&gt;
&lt;li&gt;Default human &lt;code&gt;--kraken2_db&lt;/code&gt; link has been changed from Zenodo to an AWS S3 bucket for more reliable downloads&lt;/li&gt;
&lt;li&gt;Updated pipeline template to nf-core/tools &lt;code&gt;1.14&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;Optimise MultiQC configuration and input files for faster run-time on huge sample numbers&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/122"&gt;#122&lt;/a&gt;] - Single SPAdes command to rule them all&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/138"&gt;#138&lt;/a&gt;] - Problem masking the consensus sequence&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/142"&gt;#142&lt;/a&gt;] - Unknown method invocation &lt;code&gt;toBytes&lt;/code&gt; on String type&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/169"&gt;#169&lt;/a&gt;] - ggplot2 error when generating mosdepth amplicon plot with Swift v2 primers&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/170"&gt;#170&lt;/a&gt;] - ivar trimming of Swift libraries new offset feature&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/175"&gt;#175&lt;/a&gt;] - MultiQC report does not include all the metrics&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/pull/188"&gt;#188&lt;/a&gt;] - Add and fix EditorConfig linting in entire pipeline&lt;/li&gt;
&lt;/ul&gt;
Parameters


Old parameter
New parameter




&lt;code&gt;--amplicon_bed&lt;/code&gt;
&lt;code&gt;--primer_bed&lt;/code&gt;


&lt;code&gt;--amplicon_fasta&lt;/code&gt;
&lt;code&gt;--primer_fasta&lt;/code&gt;


&lt;code&gt;--amplicon_left_suffix&lt;/code&gt;
&lt;code&gt;--primer_left_suffix&lt;/code&gt;


&lt;code&gt;--amplicon_right_suffix&lt;/code&gt;
&lt;code&gt;--primer_right_suffix&lt;/code&gt;


&lt;code&gt;--filter_dups&lt;/code&gt;
&lt;code&gt;--filter_duplicates&lt;/code&gt;


&lt;code&gt;--skip_adapter_trimming&lt;/code&gt;
&lt;code&gt;--skip_fastp&lt;/code&gt;


&lt;code&gt;--skip_amplicon_trimming&lt;/code&gt;
&lt;code&gt;--skip_cutadapt&lt;/code&gt;



&lt;code&gt;--artic_minion_aligner&lt;/code&gt;



&lt;code&gt;--artic_minion_caller&lt;/code&gt;



&lt;code&gt;--artic_minion_medaka_model&lt;/code&gt;



&lt;code&gt;--asciigenome_read_depth&lt;/code&gt;



&lt;code&gt;--asciigenome_window_size&lt;/code&gt;



&lt;code&gt;--blast_db&lt;/code&gt;



&lt;code&gt;--enable_conda&lt;/code&gt;



&lt;code&gt;--fast5_dir&lt;/code&gt;



&lt;code&gt;--fastq_dir&lt;/code&gt;



&lt;code&gt;--ivar_trim_offset&lt;/code&gt;



&lt;code&gt;--kraken2_assembly_host_filter&lt;/code&gt;



&lt;code&gt;--kraken2_variants_host_filter&lt;/code&gt;



&lt;code&gt;--min_barcode_reads&lt;/code&gt;



&lt;code&gt;--min_guppyplex_reads&lt;/code&gt;



&lt;code&gt;--multiqc_title&lt;/code&gt;



&lt;code&gt;--platform&lt;/code&gt;



&lt;code&gt;--primer_set&lt;/code&gt;



&lt;code&gt;--primer_set_version&lt;/code&gt;



&lt;code&gt;--public_data_ids&lt;/code&gt;



&lt;code&gt;--save_trimmed_fail&lt;/code&gt;



&lt;code&gt;--save_unaligned&lt;/code&gt;



&lt;code&gt;--sequencing_summary&lt;/code&gt;



&lt;code&gt;--singularity_pull_docker_container&lt;/code&gt;



&lt;code&gt;--skip_asciigenome&lt;/code&gt;



&lt;code&gt;--skip_bandage&lt;/code&gt;



&lt;code&gt;--skip_consensus&lt;/code&gt;



&lt;code&gt;--skip_ivar_trim&lt;/code&gt;



&lt;code&gt;--skip_nanoplot&lt;/code&gt;



&lt;code&gt;--skip_pangolin&lt;/code&gt;



&lt;code&gt;--skip_pycoqc&lt;/code&gt;



&lt;code&gt;--skip_nextclade&lt;/code&gt;



&lt;code&gt;--skip_sra_fastq_download&lt;/code&gt;



&lt;code&gt;--spades_hmm&lt;/code&gt;



&lt;code&gt;--spades_mode&lt;/code&gt;


&lt;code&gt;--cut_mean_quality&lt;/code&gt;



&lt;code&gt;--filter_unmapped&lt;/code&gt;



&lt;code&gt;--ivar_trim_min_len&lt;/code&gt;



&lt;code&gt;--ivar_trim_min_qual&lt;/code&gt;



&lt;code&gt;--ivar_trim_window_width&lt;/code&gt;



&lt;code&gt;--kraken2_use_ftp&lt;/code&gt;



&lt;code&gt;--max_allele_freq&lt;/code&gt;



&lt;code&gt;--min_allele_freq&lt;/code&gt;



&lt;code&gt;--min_base_qual&lt;/code&gt;



&lt;code&gt;--min_coverage&lt;/code&gt;



&lt;code&gt;--min_trim_length&lt;/code&gt;



&lt;code&gt;--minia_kmer&lt;/code&gt;



&lt;code&gt;--mpileup_depth&lt;/code&gt;



&lt;code&gt;--name&lt;/code&gt;



&lt;code&gt;--qualified_quality_phred&lt;/code&gt;



&lt;code&gt;--save_align_intermeds&lt;/code&gt;



&lt;code&gt;--save_kraken2_fastq&lt;/code&gt;



&lt;code&gt;--save_sra_fastq&lt;/code&gt;



&lt;code&gt;--skip_sra&lt;/code&gt;



&lt;code&gt;--skip_vg&lt;/code&gt;



&lt;code&gt;--unqualified_percent_limit&lt;/code&gt;



&lt;code&gt;--varscan2_strand_filter&lt;/code&gt;



&lt;blockquote&gt;&lt;p&gt;&lt;strong&gt;NB:&lt;/strong&gt; Parameter has been &lt;strong&gt;updated&lt;/strong&gt; if both old and new parameter information is present.
&lt;strong&gt;NB:&lt;/strong&gt; Parameter has been &lt;strong&gt;added&lt;/strong&gt; if just the new parameter information is present.
&lt;strong&gt;NB:&lt;/strong&gt; Parameter has been &lt;strong&gt;removed&lt;/strong&gt; if new parameter information isn't present.&lt;/p&gt;
&lt;/blockquote&gt;</description>
  </descriptions>
</resource>
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