Software Open Access

nf-core/viralrecon: nf-core/viralrecon v2.5 - Manganese Monkey

Harshil Patel; Sarai Varona; Sara Monzón; Jose Espinosa-Carrasco; Michael L Heuer; nf-core bot; Anthony Underwood; Gisela Gabernet; Phil Ewels; MiguelJulia; Stephen Kelly; Stevin Wilson; Erika; Katrin Sameith; Maxime U. Garcia; jcurado; Kevin Menden


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    <subfield code="a">[&lt;a href="https://github.com/nf-core/viralrecon/releases/tag/2.5"&gt;2.5&lt;/a&gt;] - 2022-07-13
Enhancements &amp;amp; fixes
&lt;ul&gt;
&lt;li&gt;Default Nextclade dataset shipped with the pipeline has been bumped from &lt;code&gt;2022-01-18T12:00:00Z&lt;/code&gt; -&amp;gt; &lt;code&gt;2022-06-14T12:00:00Z&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/234"&gt;#234&lt;/a&gt;] - Remove replacement of dashes in sample name with underscores&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/292"&gt;#292&lt;/a&gt;] - Filter empty FastQ files after adapter trimming&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/pull/303"&gt;#303&lt;/a&gt;] - New pangolin dbs (4.0.x) not assigning lineages to Sars-CoV-2 samples in MultiQC report correctly&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/pull/304"&gt;#304&lt;/a&gt;] - Re-factor code of &lt;code&gt;ivar_variants_to_vcf&lt;/code&gt; script&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/306"&gt;#306&lt;/a&gt;] - Add contig field information in vcf header in ivar_variants_to_vcf and use bcftools sort&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/311"&gt;#311&lt;/a&gt;] - Invalid declaration val medaka_model_string&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/viralrecon/issues/316"&gt;#316&lt;/a&gt;] - Variant calling isn't run when using --skip_asciigenome with metagenomic data&lt;/li&gt;
&lt;li&gt;[&lt;a href="https://github.com/nf-core/rnaseq/issues/764"&gt;nf-core/rnaseq#764&lt;/a&gt;] - Test fails when using GCP due to missing tools in the basic biocontainer&lt;/li&gt;
&lt;li&gt;Updated pipeline template to &lt;a href="https://github.com/nf-core/tools/releases/tag/2.4.1"&gt;nf-core/tools 2.4.1&lt;/a&gt;&lt;/li&gt;
&lt;/ul&gt;
Software dependencies
&lt;p&gt;Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own &lt;a href="https://biocontainers.pro/#/registry"&gt;Biocontainer&lt;/a&gt;. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.&lt;/p&gt;
&lt;table&gt;
&lt;thead&gt;&lt;tr&gt;
&lt;th&gt;Dependency&lt;/th&gt;
&lt;th&gt;Old version&lt;/th&gt;
&lt;th&gt;New version&lt;/th&gt;
&lt;/tr&gt;
&lt;/thead&gt;
&lt;tbody&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;artic&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;1.2.1&lt;/td&gt;
&lt;td&gt;1.2.2&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;bcftools&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;1.14&lt;/td&gt;
&lt;td&gt;1.15.1&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;multiqc&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;1.11&lt;/td&gt;
&lt;td&gt;1.13a&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;nanoplot&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;1.39.0&lt;/td&gt;
&lt;td&gt;1.40.0&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;nextclade&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;1.10.2&lt;/td&gt;
&lt;td&gt;2.2.0&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;pangolin&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;3.1.20&lt;/td&gt;
&lt;td&gt;4.1.1&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;picard&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;2.26.10&lt;/td&gt;
&lt;td&gt;2.27.4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;quast&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;5.0.2&lt;/td&gt;
&lt;td&gt;5.2.0&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;samtools&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;1.14&lt;/td&gt;
&lt;td&gt;1.15.1&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;spades&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;3.15.3&lt;/td&gt;
&lt;td&gt;3.15.4&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
&lt;td&gt;&lt;code&gt;vcflib&lt;/code&gt;&lt;/td&gt;
&lt;td&gt;1.0.2&lt;/td&gt;
&lt;td&gt;1.0.3&lt;/td&gt;
&lt;/tr&gt;
&lt;/tbody&gt;
&lt;/table&gt;
&lt;blockquote&gt;&lt;p&gt;&lt;strong&gt;NB:&lt;/strong&gt; Dependency has been &lt;strong&gt;updated&lt;/strong&gt; if both old and new version information is present.&lt;/p&gt;
&lt;p&gt;&lt;strong&gt;NB:&lt;/strong&gt; Dependency has been &lt;strong&gt;added&lt;/strong&gt; if just the new version information is present.&lt;/p&gt;
&lt;p&gt;&lt;strong&gt;NB:&lt;/strong&gt; Dependency has been &lt;strong&gt;removed&lt;/strong&gt; if new version information isn't present.&lt;/p&gt;
&lt;/blockquote&gt;</subfield>
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