Published May 13, 2021
| Version 2.0
Software
Open
nf-core/viralrecon: nf-core/viralrecon v2.0 - Silver Ferret
Creators
- 1. The Francis Crick Institute
- 2. BU-ISCIII
- 3. UC Berkeley AMPLab/RISE Lab
- 4. @qbicsoftware
- 5. Science for Life Laboratory
- 6. DRESDEN-concept Genome Center
- 7. @SciLifeLab | Karolinska Institutet
- 8. @Flomics
Description
[2.0] - 2021-05-13 :warning: 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
- 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
--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.
Files
nf-core/viralrecon-2.0.zip
Files
(3.0 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/nf-core/viralrecon/tree/2.0 (URL)