Assembly and intrahost/low-frequency variant calling for viral samples
Special thanks to the following for their code contributions to the release:
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
--skip_asciigenome
with metagenomic dataivar_variants_to_vcf
: Ignore lines without annotation in ivar tsv fileworkflow.onComplete
event handlerivar_variants_to_vcf
script: Duplicated positions in tsv file due to overlapping annotationsartic/minion
and artic/guppyplex
: Update module version 1.2.2 -> 1.2.3tower.yml
for Report rendering in Nextflow Tower--skip_plasmidid
by defaultOld parameter | New parameter |
---|---|
--tracedir |
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.
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 |
---|---|---|
artic |
1.2.2 | 1.2.3 |
bcftools |
1.51.1 | 1.16 |
blast |
2.12.0 | 2.13.0 |
cutadapt |
3.5 | 4.2 |
ivar |
1.3.1 | 1.4 |
multiqc |
1.13a | 1.14 |
nanoplot |
1.40.0 | 1.41.0 |
nextclade |
2.2.0 | 2.12.0 |
pangolin |
4.1.1 | 4.2 |
picard |
2.27.4 | 3.0.0 |
samtools |
1.15.1 | 1.16.1 |
spades |
3.15.4 | 3.15.5 |
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.
2022-01-18T12:00:00Z
-> 2022-06-14T12:00:00Z
ivar_variants_to_vcf
scriptNote, 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 |
---|---|---|
artic |
1.2.1 | 1.2.2 |
bcftools |
1.14 | 1.15.1 |
multiqc |
1.11 | 1.13a |
nanoplot |
1.39.0 | 1.40.0 |
nextclade |
1.10.2 | 2.2.0 |
pangolin |
3.1.20 | 4.1.1 |
picard |
2.26.10 | 2.27.4 |
quast |
5.0.2 | 5.2.0 |
samtools |
1.14 | 1.15.1 |
spades |
3.15.3 | 3.15.4 |
vcflib |
1.0.2 | 1.0.3 |
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.
--outdir
a mandatory parameterOld parameter | New parameter |
---|---|
--publish_dir_mode |
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.
--protocol amplicon
, in the previous release, iVar was used for both the variant calling and consensus sequence generation. The pipeline will now perform the variant calling and consensus sequence generation with iVar and BCFTools/BEDTools, respectively.21.04.0
-> 21.10.3
Old parameter | New parameter |
---|---|
--nextclade_dataset |
|
--nextclade_dataset_name |
|
--nextclade_dataset_reference |
|
--nextclade_dataset_tag |
|
--skip_consensus_plots |
|
--skip_variants_long_table |
|
--consensus_caller |
|
--callers |
--variant_caller |
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.
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 |
---|---|---|
bcftools |
1.11 | 1.14 |
blast |
2.10.1 | 2.12.0 |
bowtie2 |
2.4.2 | 2.4.4 |
cutadapt |
3.2 | 3.5 |
fastp |
0.20.1 | 0.23.2 |
kraken2 |
2.1.1 | 2.1.2 |
minia |
3.2.4 | 3.2.6 |
mosdepth |
0.3.1 | 0.3.2 |
nanoplot |
1.36.1 | 1.39.0 |
nextclade |
1.10.2 | |
pangolin |
3.1.7 | 3.1.19 |
picard |
2.23.9 | 2.26.10 |
python |
3.8.3 | 3.9.5 |
samtools |
1.10 | 1.14 |
spades |
3.15.2 | 3.15.3 |
tabix |
0.2.6 | 1.11 |
vcflib |
1.0.2 |
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.
PYCOQC.out
is undefinedOld 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.
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.
v21.04.0
(see nextflow#572)--callers
parameter.--kraken2_db
link has been changed from Zenodo to an AWS S3 bucket for more reliable downloads1.14
toBytes
on String typeOld 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.
Added
--min_mapped_reads
to circumvent failures for samples with low number of mapped reads--varscan2_strand_filter
to toggle the default Varscan 2 strand filter--skip_mosdepth
- skip genome-wide and amplicon coverage plot generation from mosdepth output--amplicon_left_suffix
- to provide left primer suffix used in name field of --amplicon_bed
--amplicon_right_suffix
- to provide right primer suffix used in name field of --amplicon_bed
--min_allele_freq
- minimum allele frequency threshold for calling variants--mpileup_depth
- SAMTools mpileup max per-file depth--ivar_exclude_reads
renamed to --ivar_trim_noprimer
--ivar_trim_min_len
- minimum length of read to retain after primer trimming--ivar_trim_min_qual
- minimum quality threshold for sliding window to pass--ivar_trim_window_width
- width of sliding windowRemoved
--skip_qc
parameterDependencies
0.2.6
2.2.0
2.54.0
1.6.6
1.1.0
1.3.0
3.3.1
1.4.4
0.5.1
2.10.3
-> 2.10.7
2.3.5.1
-> 2.4.1
2.22.8
-> 2.23.0
3.2.3
-> 3.2.4
1.5.2
-> 1.6.3