nf-core/viralrecon v2.0 - Silver Ferret

[2.0] - 2021-05-13

⚠️ 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 & 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.