nf-core/viralrecon: nf-core/viralrecon v2.1 - Lead Mink

[2.1] - 2021-06-15 Enhancements & fixes

• Removed workflow to download data from public databases in favour of using nf-core/fetchngs
• Added Pangolin results to MultiQC report
• Added docs about structure of data required for running Nanopore data
• Added docs about using other primer sets for Illumina data
• Added warning to MultiQC report for samples that have no reads after adapter trimming
• Added docs about overwriting default container definitions to use latest versions e.g. Pangolin
• Dashes and spaces in sample names will be converted to underscores to avoid issues when creating the summary metrics
• [#196] - Add mosdepth heatmap to MultiQC report
• [#197] - Output a .tsv comprising the Nextclade and Pangolin results for all samples processed
• [#198] - ASCIIGenome failing during analysis
• [#201] - Conditional include are not expected to work
• [#204] - Memory errors for SNP_EFF step

Parameters Old parameter New parameter --public_data_ids --skip_sra_fastq_download

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.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. 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.

Dependency Old version New version nextclade_js 0.14.2 0.14.4 pangolin 2.4.2 3.0.5

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if new version information isn't present.