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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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    "description": "[<a href=\"https://github.com/nf-core/rnaseq/releases/tag/2.0\">2.0</a>] - 2021-05-13\n:warning: Major enhancements\n<ul>\n<li>Pipeline has been re-implemented in <a href=\"https://www.nextflow.io/docs/latest/dsl2.html\">Nextflow DSL2</a></li>\n<li>All software containers are now exclusively obtained from <a href=\"https://biocontainers.pro/#/registry\">Biocontainers</a></li>\n<li>Updated minimum Nextflow version to <code>v21.04.0</code> (see <a href=\"https://github.com/nextflow-io/nextflow/issues/1964\">nextflow#572</a>)</li>\n<li><a href=\"http://samtools.github.io/bcftools/bcftools.html\">BCFtools</a> and <a href=\"https://github.com/andersen-lab/ivar\">iVar</a> will be run by default for Illumina metagenomics and amplicon data, respectively. However, this behaviour can be customised with the <code>--callers</code> parameter.</li>\n<li>Variant graph processes to call variants relative to the reference genome directly from <em>de novo</em> assemblies have been deprecated and removed</li>\n<li>Variant calling with Varscan 2 has been deprecated and removed due to <a href=\"https://github.com/dkoboldt/varscan/issues/12\">licensing restrictions</a></li>\n<li>New tools:<ul>\n<li><a href=\"https://github.com/cov-lineages/pangolin\">Pangolin</a> for lineage analysis</li>\n<li><a href=\"https://github.com/nextstrain/nextclade\">Nextclade</a> for clade assignment, mutation calling and consensus sequence quality checks</li>\n<li><a href=\"https://asciigenome.readthedocs.io/en/latest/\">ASCIIGenome</a> for individual variant screenshots with annotation tracks</li>\n</ul>\n</li>\n</ul>\nOther enhancements &amp; fixes\n<ul>\n<li>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</li>\n<li>Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation</li>\n<li>Default human <code>--kraken2_db</code> link has been changed from Zenodo to an AWS S3 bucket for more reliable downloads</li>\n<li>Updated pipeline template to nf-core/tools <code>1.14</code></li>\n<li>Optimise MultiQC configuration and input files for faster run-time on huge sample numbers</li>\n<li>[<a href=\"https://github.com/nf-core/viralrecon/issues/122\">#122</a>] - Single SPAdes command to rule them all</li>\n<li>[<a href=\"https://github.com/nf-core/viralrecon/issues/138\">#138</a>] - Problem masking the consensus sequence</li>\n<li>[<a href=\"https://github.com/nf-core/viralrecon/issues/142\">#142</a>] - Unknown method invocation <code>toBytes</code> on String type</li>\n<li>[<a href=\"https://github.com/nf-core/viralrecon/issues/169\">#169</a>] - ggplot2 error when generating mosdepth amplicon plot with Swift v2 primers</li>\n<li>[<a href=\"https://github.com/nf-core/viralrecon/issues/170\">#170</a>] - ivar trimming of Swift libraries new offset feature</li>\n<li>[<a href=\"https://github.com/nf-core/viralrecon/issues/175\">#175</a>] - MultiQC report does not include all the metrics</li>\n<li>[<a href=\"https://github.com/nf-core/viralrecon/pull/188\">#188</a>] - Add and fix EditorConfig linting in entire pipeline</li>\n</ul>\nParameters\n\n\nOld parameter\nNew parameter\n\n\n\n\n<code>--amplicon_bed</code>\n<code>--primer_bed</code>\n\n\n<code>--amplicon_fasta</code>\n<code>--primer_fasta</code>\n\n\n<code>--amplicon_left_suffix</code>\n<code>--primer_left_suffix</code>\n\n\n<code>--amplicon_right_suffix</code>\n<code>--primer_right_suffix</code>\n\n\n<code>--filter_dups</code>\n<code>--filter_duplicates</code>\n\n\n<code>--skip_adapter_trimming</code>\n<code>--skip_fastp</code>\n\n\n<code>--skip_amplicon_trimming</code>\n<code>--skip_cutadapt</code>\n\n\n\n<code>--artic_minion_aligner</code>\n\n\n\n<code>--artic_minion_caller</code>\n\n\n\n<code>--artic_minion_medaka_model</code>\n\n\n\n<code>--asciigenome_read_depth</code>\n\n\n\n<code>--asciigenome_window_size</code>\n\n\n\n<code>--blast_db</code>\n\n\n\n<code>--enable_conda</code>\n\n\n\n<code>--fast5_dir</code>\n\n\n\n<code>--fastq_dir</code>\n\n\n\n<code>--ivar_trim_offset</code>\n\n\n\n<code>--kraken2_assembly_host_filter</code>\n\n\n\n<code>--kraken2_variants_host_filter</code>\n\n\n\n<code>--min_barcode_reads</code>\n\n\n\n<code>--min_guppyplex_reads</code>\n\n\n\n<code>--multiqc_title</code>\n\n\n\n<code>--platform</code>\n\n\n\n<code>--primer_set</code>\n\n\n\n<code>--primer_set_version</code>\n\n\n\n<code>--public_data_ids</code>\n\n\n\n<code>--save_trimmed_fail</code>\n\n\n\n<code>--save_unaligned</code>\n\n\n\n<code>--sequencing_summary</code>\n\n\n\n<code>--singularity_pull_docker_container</code>\n\n\n\n<code>--skip_asciigenome</code>\n\n\n\n<code>--skip_bandage</code>\n\n\n\n<code>--skip_consensus</code>\n\n\n\n<code>--skip_ivar_trim</code>\n\n\n\n<code>--skip_nanoplot</code>\n\n\n\n<code>--skip_pangolin</code>\n\n\n\n<code>--skip_pycoqc</code>\n\n\n\n<code>--skip_nextclade</code>\n\n\n\n<code>--skip_sra_fastq_download</code>\n\n\n\n<code>--spades_hmm</code>\n\n\n\n<code>--spades_mode</code>\n\n\n<code>--cut_mean_quality</code>\n\n\n\n<code>--filter_unmapped</code>\n\n\n\n<code>--ivar_trim_min_len</code>\n\n\n\n<code>--ivar_trim_min_qual</code>\n\n\n\n<code>--ivar_trim_window_width</code>\n\n\n\n<code>--kraken2_use_ftp</code>\n\n\n\n<code>--max_allele_freq</code>\n\n\n\n<code>--min_allele_freq</code>\n\n\n\n<code>--min_base_qual</code>\n\n\n\n<code>--min_coverage</code>\n\n\n\n<code>--min_trim_length</code>\n\n\n\n<code>--minia_kmer</code>\n\n\n\n<code>--mpileup_depth</code>\n\n\n\n<code>--name</code>\n\n\n\n<code>--qualified_quality_phred</code>\n\n\n\n<code>--save_align_intermeds</code>\n\n\n\n<code>--save_kraken2_fastq</code>\n\n\n\n<code>--save_sra_fastq</code>\n\n\n\n<code>--skip_sra</code>\n\n\n\n<code>--skip_vg</code>\n\n\n\n<code>--unqualified_percent_limit</code>\n\n\n\n<code>--varscan2_strand_filter</code>\n\n\n\n<blockquote><p><strong>NB:</strong> Parameter has been <strong>updated</strong> if both old and new parameter information is present.\n<strong>NB:</strong> Parameter has been <strong>added</strong> if just the new parameter information is present.\n<strong>NB:</strong> Parameter has been <strong>removed</strong> if new parameter information isn't present.</p>\n</blockquote>", 
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