viral-ngs: genomic analysis pipelines for viral sequencing¶

Contents¶

Description of the methods¶

Taxonomic read filtration¶

Human, contaminant, and duplicate read removal¶

The assembly pipeline begins by depleting paired-end reads from each sample of human and other contaminants using BMTAGGER and BLASTN, and removing PCR duplicates using M-Vicuna (a custom version of Vicuna).

Taxonomic selection¶

Reads are then filtered to to a genus-level database using LASTAL, quality-trimmed with Trimmomatic, and further deduplicated with PRINSEQ.

Viral genome analysis¶

Viral genome assembly¶

The filtered and trimmed reads are subsampled to at most 100,000 pairs. de novo assemby is performed using Trinity. SPAdes is also offered as an alternative de novo assembler. Reference-assisted assembly improvements follow (contig scaffolding, orienting, etc.) with MUMMER and MUSCLE or MAFFT. Gap2Seq is used to seal gaps between scaffolded de novo contigs with sequencing reads.

Each sample’s reads are aligned to its de novo assembly using Novoalign and any remaining duplicates were removed using Picard MarkDuplicates. Variant positions in each assembly were identified using GATK IndelRealigner and UnifiedGenotyper on the read alignments. The assembly was refined to represent the major allele at each variant site, and any positions supported by fewer than three reads were changed to N.

This align-call-refine cycle is iterated twice, to minimize reference bias in the assembly.

Intrahost variant identification¶

Intrahost variants (iSNVs) were called from each sample’s read alignments using V-Phaser2 and subjected to an initial set of filters: variant calls with fewer than five forward or reverse reads or more than a 10-fold strand bias were eliminated. iSNVs were also removed if there was more than a five-fold difference between the strand bias of the variant call and the strand bias of the reference call. Variant calls that passed these filters were additionally subjected to a 0.5% frequency filter. The final list of iSNVs contains only variant calls that passed all filters in two separate library preparations. These files infer 100% allele frequencies for all samples at an iSNV position where there was no intra-host variation within the sample, but a clear consensus call during assembly. Annotations are computed with snpEff.

Taxonomic read identification¶

Metagenomic classifiers include Kraken and Diamond. In each case, results are visualized with Krona.

Using the WDL pipelines¶

Rather than chaining together viral-ngs pipeline steps as series of tool commands called in isolation, it is possible to execute them as a complete automated pipeline, from processing raw sequencer output to creating files suitable for GenBank submission. This utilizes the Workflow Description Language, which is documented at: https://github.com/openwdl/wdl

There are various methods for executing these workflows on your infrastructure which are more thoroughly documented in our README.

WDL Workflows¶

Documentation for each workflow is provided here. Although there are many workflows that serve different functions, some of the primary workflows we use most often include:

align_and_count_report¶

Inputs¶

Required inputs¶

align_and_count_report.align_and_count.reads_bam
File — Default: None
???

align_and_count_report.align_and_count.ref_db
File — Default: None
???

Other inputs¶

Show/Hide

align_and_count_report.align_and_count.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

align_and_count_report.align_and_count.machine_mem_gb
Int? — Default: None
???

align_and_count_report.align_and_count.minScoreToFilter
Int? — Default: 60
???

align_and_count_report.align_and_count.topNHits
Int? — Default: 3
???

align_and_plot¶

Inputs¶

Required inputs¶

align_and_plot.align.reads_unmapped_bam
File — Default: None
???

align_and_plot.align.reference_fasta
File — Default: None
???

Other inputs¶

Show/Hide

align_and_plot.align.aligner
String? — Default: "novoalign"
Short read aligner to use: novoalign or bwa. (Default: novoalign)

align_and_plot.align.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

align_and_plot.align.novocraft_license
File? — Default: None
???

align_and_plot.align.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

align_and_plot.align.skip_mark_dupes
Boolean? — Default: false
???

align_and_plot.aligner_options
String? — Default: "-r Random -l 30 -g 40 -x 20 -t 502"
???

align_and_plot.plot_coverage.bin_large_plots
Boolean? — Default: false
???

align_and_plot.plot_coverage.binning_summary_statistic
String? — Default: "max"
???

align_and_plot.plot_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

align_and_plot.plot_coverage.plot_only_non_duplicates
Boolean? — Default: false
???

align_and_plot.plot_coverage.skip_mark_dupes
Boolean? — Default: false
???

assemble_denovo¶

Inputs¶

Required inputs¶

assemble_denovo.reads_unmapped_bam
File — Default: None
???

assemble_denovo.reference_genome_fasta
Array[File]+ — Default: None
After denovo assembly, large contigs are scaffolded against a reference genome to determine orientation and to join contigs together, before further polishing by reads. You must supply at least one reference genome (all segments/chromomes in a single fasta file). If more than one reference is provided, contigs will be scaffolded against all of them and the one with the most complete assembly will be chosen for downstream polishing.

assemble_denovo.trim_clip_db
File — Default: None
???

Other inputs¶

Show/Hide

assemble_denovo.assemble.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

assemble_denovo.assemble.machine_mem_gb
Int? — Default: None
???

assemble_denovo.assemble.spades_min_contig_len
Int? — Default: 0
???

assemble_denovo.assemble.spades_n_reads
Int? — Default: 10000000
???

assemble_denovo.assemble.trinity_n_reads
Int? — Default: 250000
???

assemble_denovo.assembler
String — Default: "spades"
???

assemble_denovo.call_isnvs
Boolean — Default: false
???

assemble_denovo.deplete_blastDbs
Array[File] — Default: []
Optional list of databases to use for blastn-based depletion. Sequences in fasta format will be indexed on the fly, pre-blast-indexed databases may be provided as tarballs.

assemble_denovo.deplete_bmtaggerDbs
Array[File] — Default: []
Optional list of databases to use for bmtagger-based depletion. Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.

assemble_denovo.deplete_bwaDbs
Array[File] — Default: []
Optional list of databases to use for bwa mem-based depletion. Sequences in fasta format will be indexed on the fly, pre-bwa-indexed databases may be provided as tarballs.

assemble_denovo.deplete_taxa.clear_tags
Boolean? — Default: false
???

assemble_denovo.deplete_taxa.cpu
Int? — Default: 8
???

assemble_denovo.deplete_taxa.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

assemble_denovo.deplete_taxa.machine_mem_gb
Int? — Default: None
???

assemble_denovo.deplete_taxa.query_chunk_size
Int? — Default: None
???

assemble_denovo.deplete_taxa.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

assemble_denovo.filter_to_taxon.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

assemble_denovo.filter_to_taxon.error_on_reads_in_neg_control
Boolean? — Default: false
???

assemble_denovo.filter_to_taxon.machine_mem_gb
Int? — Default: None
???

assemble_denovo.filter_to_taxon.neg_control_prefixes_space_separated
String? — Default: "neg water NTC"
???

assemble_denovo.filter_to_taxon.negative_control_reads_threshold
Int? — Default: 0
???

assemble_denovo.filter_to_taxon_db
File? — Default: None
Optional database to use to filter read set to those that match by LASTAL. Sequences in fasta format will be indexed on the fly.

assemble_denovo.isnvs_per_sample.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

assemble_denovo.isnvs_per_sample.machine_mem_gb
Int? — Default: None
???

assemble_denovo.isnvs_per_sample.maxBias
Int? — Default: None
???

assemble_denovo.isnvs_per_sample.minReadsPerStrand
Int? — Default: None
???

assemble_denovo.isnvs_per_sample.sample_name
String — Default: basename(basename(basename(mapped_bam,".bam"),".all"),".mapped")
???

assemble_denovo.isnvs_per_sample.threads
Int? — Default: None
???

assemble_denovo.novocraft_license
File? — Default: None
???

assemble_denovo.nucmer_max_gap
Int? — Default: None
???

assemble_denovo.nucmer_min_cluster
Int? — Default: None
???

assemble_denovo.nucmer_min_match
Int? — Default: None
???

assemble_denovo.refine_2x_and_plot.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

assemble_denovo.refine_2x_and_plot.machine_mem_gb
Int? — Default: None
???

assemble_denovo.refine_2x_and_plot.plot_coverage_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100 -k"
???

assemble_denovo.refine_2x_and_plot.refine1_major_cutoff
Float? — Default: 0.5
???

assemble_denovo.refine_2x_and_plot.refine1_min_coverage
Int? — Default: 2
???

assemble_denovo.refine_2x_and_plot.refine1_novoalign_options
String? — Default: "-r Random -l 30 -g 40 -x 20 -t 502"
???

assemble_denovo.refine_2x_and_plot.refine2_major_cutoff
Float? — Default: 0.5
???

assemble_denovo.refine_2x_and_plot.refine2_min_coverage
Int? — Default: 3
???

assemble_denovo.refine_2x_and_plot.refine2_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100"
???

assemble_denovo.rmdup_ubam.docker
String? — Default: "quay.io/broadinstitute/viral-core"
???

assemble_denovo.rmdup_ubam.machine_mem_gb
Int? — Default: None
???

assemble_denovo.rmdup_ubam.method
String — Default: "mvicuna"
mvicuna or cdhit

assemble_denovo.scaffold.aligner
String? — Default: None
???

assemble_denovo.scaffold.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

assemble_denovo.scaffold.machine_mem_gb
Int? — Default: None
???

assemble_denovo.scaffold.sample_name
String — Default: basename(basename(basename(contigs_fasta,".fasta"),".assembly1-trinity"),".assembly1-spades")
???

assemble_denovo.scaffold_min_length_fraction
Float? — Default: None
???

assemble_denovo.scaffold_min_pct_contig_aligned
Float? — Default: None
???

assemble_denovo.scaffold_min_unambig
Float? — Default: None
???

assemble_denovo.scaffold_replace_length
Int? — Default: 55
???

assemble_refbased¶

Reference-based microbial consensus calling. Aligns short reads to a singular reference genome, calls a new consensus sequence, and emits: new assembly, reads aligned to provided reference, reads aligned to new assembly, various figures of merit, plots, and QC metrics. The user may provide unaligned reads spread across multiple input files and this workflow will parallelize alignment per input file before merging results prior to consensus calling.

Inputs¶

Required inputs¶

assemble_refbased.reads_unmapped_bams
Array[File]+ — Default: None
Unaligned reads in BAM format

assemble_refbased.reference_fasta
File — Default: None
Reference genome to align reads to.

assemble_refbased.sample_name
String — Default: None
Base name of output files. The 'SM' field in BAM read group headers are also rewritten to this value. Avoid spaces and other filename-unfriendly characters.

Other inputs¶

Show/Hide

assemble_refbased.align_to_ref.aligner
String? — Default: "novoalign"
Short read aligner to use: novoalign or bwa. (Default: novoalign)

assemble_refbased.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.align_to_ref.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

assemble_refbased.align_to_self.aligner
String? — Default: "novoalign"
Short read aligner to use: novoalign or bwa. (Default: novoalign)

assemble_refbased.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.align_to_self.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

assemble_refbased.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

assemble_refbased.call_consensus.machine_mem_gb
Int? — Default: None
???

assemble_refbased.call_consensus.major_cutoff
Float? — Default: 0.5
???

assemble_refbased.call_consensus.mark_duplicates
Boolean? — Default: false
???

assemble_refbased.call_consensus.min_coverage
Int? — Default: 2
???

assemble_refbased.ivar_trim.docker
String — Default: "andersenlabapps/ivar:1.2.1"
???

assemble_refbased.ivar_trim.machine_mem_gb
Int? — Default: None
???

assemble_refbased.ivar_trim.min_keep_length
Int? — Default: None
Minimum length of read to retain after trimming (Default: 30)

assemble_refbased.ivar_trim.min_quality
Int? — Default: None
Minimum quality threshold for sliding window to pass (Default: 20)

assemble_refbased.ivar_trim.sliding_window
Int? — Default: None
Width of sliding window for quality trimming (Default: 4)

assemble_refbased.merge_align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.merge_align_to_ref.reheader_table
File? — Default: None
???

assemble_refbased.merge_align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.merge_align_to_self.reheader_table
File? — Default: None
???

assemble_refbased.multiqc_align_to_ref.comment
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.config
File? — Default: None
???

assemble_refbased.multiqc_align_to_ref.config_yaml
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.data_dir
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

assemble_refbased.multiqc_align_to_ref.exclude_modules
Array[String]+? — Default: None
???

assemble_refbased.multiqc_align_to_ref.export
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.file_name
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.flat
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.force
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.full_names
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.ignore_analysis_files
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.ignore_sample_names
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.interactive
Boolean — Default: true
???

assemble_refbased.multiqc_align_to_ref.lint
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.megaQC_upload
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.module_to_use
Array[String]+? — Default: None
???

assemble_refbased.multiqc_align_to_ref.no_data_dir
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.out_dir
String — Default: "./multiqc-output"
???

assemble_refbased.multiqc_align_to_ref.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

assemble_refbased.multiqc_align_to_ref.pdf
Boolean — Default: false
???

assemble_refbased.multiqc_align_to_ref.sample_names
File? — Default: None
???

assemble_refbased.multiqc_align_to_ref.tag
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.template
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.title
String? — Default: None
???

assemble_refbased.multiqc_align_to_ref.zip_data_dir
Boolean — Default: false
???

assemble_refbased.novocraft_license
File? — Default: None
The default Novoalign short read aligner is a commercially licensed software that is available in a much slower, single-threaded version for free. If you have a paid license file, provide it here to run in multi-threaded mode. If this is omitted, it will run in single-threaded mode.

assemble_refbased.plot_ref_coverage.bin_large_plots
Boolean? — Default: false
???

assemble_refbased.plot_ref_coverage.binning_summary_statistic
String? — Default: "max"
???

assemble_refbased.plot_ref_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.plot_ref_coverage.plot_only_non_duplicates
Boolean? — Default: false
???

assemble_refbased.plot_ref_coverage.skip_mark_dupes
Boolean? — Default: false
???

assemble_refbased.plot_self_coverage.bin_large_plots
Boolean? — Default: false
???

assemble_refbased.plot_self_coverage.binning_summary_statistic
String? — Default: "max"
???

assemble_refbased.plot_self_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

assemble_refbased.plot_self_coverage.plot_only_non_duplicates
Boolean? — Default: false
???

assemble_refbased.plot_self_coverage.skip_mark_dupes
Boolean? — Default: false
???

assemble_refbased.skip_mark_dupes
Boolean? — Default: false
skip Picard MarkDuplicates step after alignment. This is recommended to be set to true for PCR amplicon based data. (Default: false)

assemble_refbased.trim_coords_bed
File? — Default: None
optional primers to trim in reference coordinate space (0-based BED format)

bams_multiqc¶

Inputs¶

Required inputs¶

bams_multiqc.read_bams
Array[File]+ — Default: None
???

Other inputs¶

Show/Hide

bams_multiqc.fastqc.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

bams_multiqc.MultiQC.comment
String? — Default: None
???

bams_multiqc.MultiQC.config
File? — Default: None
???

bams_multiqc.MultiQC.config_yaml
String? — Default: None
???

bams_multiqc.MultiQC.data_dir
Boolean — Default: false
???

bams_multiqc.MultiQC.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

bams_multiqc.MultiQC.exclude_modules
Array[String]+? — Default: None
???

bams_multiqc.MultiQC.export
Boolean — Default: false
???

bams_multiqc.MultiQC.file_name
String? — Default: None
???

bams_multiqc.MultiQC.flat
Boolean — Default: false
???

bams_multiqc.MultiQC.force
Boolean — Default: false
???

bams_multiqc.MultiQC.full_names
Boolean — Default: false
???

bams_multiqc.MultiQC.ignore_analysis_files
String? — Default: None
???

bams_multiqc.MultiQC.ignore_sample_names
String? — Default: None
???

bams_multiqc.MultiQC.interactive
Boolean — Default: true
???

bams_multiqc.MultiQC.lint
Boolean — Default: false
???

bams_multiqc.MultiQC.megaQC_upload
Boolean — Default: false
???

bams_multiqc.MultiQC.module_to_use
Array[String]+? — Default: None
???

bams_multiqc.MultiQC.no_data_dir
Boolean — Default: false
???

bams_multiqc.MultiQC.out_dir
String — Default: "./multiqc-output"
???

bams_multiqc.MultiQC.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

bams_multiqc.MultiQC.pdf
Boolean — Default: false
???

bams_multiqc.MultiQC.sample_names
File? — Default: None
???

bams_multiqc.MultiQC.tag
String? — Default: None
???

bams_multiqc.MultiQC.template
String? — Default: None
???

bams_multiqc.MultiQC.title
String? — Default: None
???

bams_multiqc.MultiQC.zip_data_dir
Boolean — Default: false
???

build_augur_tree¶

Inputs¶

Required inputs¶

build_augur_tree.assembly_fastas
Array[File] — Default: None
???

build_augur_tree.export_auspice_json.auspice_config
File — Default: None
???

build_augur_tree.genbank_gb
File — Default: None
???

build_augur_tree.metadata
File — Default: None
???

build_augur_tree.ref_fasta
File — Default: None
???

build_augur_tree.virus
String — Default: None
???

Other inputs¶

Show/Hide

build_augur_tree.ancestral_tree.docker
String — Default: "nextstrain/base"
???

build_augur_tree.ancestral_tree.infer_ambiguous
Boolean? — Default: false
???

build_augur_tree.ancestral_tree.inference
String? — Default: None
???

build_augur_tree.ancestral_tree.keep_ambiguous
Boolean? — Default: false
???

build_augur_tree.ancestral_tree.keep_overhangs
Boolean? — Default: false
???

build_augur_tree.ancestral_tree.machine_mem_gb
Int? — Default: None
???

build_augur_tree.ancestral_tree.output_vcf
File? — Default: None
???

build_augur_tree.ancestral_tree.vcf_reference
File? — Default: None
???

build_augur_tree.augur_mafft_align.debug
Boolean? — Default: false
???

build_augur_tree.augur_mafft_align.docker
String — Default: "nextstrain/base"
???

build_augur_tree.augur_mafft_align.existing_alignment
Boolean? — Default: false
???

build_augur_tree.augur_mafft_align.fill_gaps
Boolean? — Default: true
???

build_augur_tree.augur_mafft_align.machine_mem_gb
Int? — Default: None
???

build_augur_tree.augur_mafft_align.remove_reference
Boolean? — Default: true
???

build_augur_tree.draft_augur_tree.docker
String — Default: "nextstrain/base"
???

build_augur_tree.draft_augur_tree.exclude_sites
File? — Default: None
???

build_augur_tree.draft_augur_tree.machine_mem_gb
Int? — Default: None
???

build_augur_tree.draft_augur_tree.method
String? — Default: None
???

build_augur_tree.draft_augur_tree.substitution_model
String? — Default: None
???

build_augur_tree.draft_augur_tree.vcf_reference
File? — Default: None
???

build_augur_tree.export_auspice_json.docker
String — Default: "nextstrain/base"
???

build_augur_tree.export_auspice_json.machine_mem_gb
Int? — Default: None
???

build_augur_tree.refine_augur_tree.branch_length_inference
String? — Default: None
???

build_augur_tree.refine_augur_tree.clock_filter_iqd
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.clock_rate
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.clock_std_dev
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.covariance
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.date_confidence
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.date_inference
String? — Default: None
???

build_augur_tree.refine_augur_tree.divergence_units
String? — Default: None
???

build_augur_tree.refine_augur_tree.docker
String — Default: "nextstrain/base"
???

build_augur_tree.refine_augur_tree.gen_per_year
Int? — Default: None
???

build_augur_tree.refine_augur_tree.keep_polytomies
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.keep_root
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.machine_mem_gb
Int? — Default: None
???

build_augur_tree.refine_augur_tree.no_covariance
Boolean? — Default: false
???

build_augur_tree.refine_augur_tree.precision
Int? — Default: None
???

build_augur_tree.refine_augur_tree.root
String? — Default: None
???

build_augur_tree.refine_augur_tree.vcf_reference
File? — Default: None
???

build_augur_tree.translate_augur_tree.docker
String — Default: "nextstrain/base"
???

build_augur_tree.translate_augur_tree.genes
File? — Default: None
???

build_augur_tree.translate_augur_tree.machine_mem_gb
Int? — Default: None
???

build_augur_tree.translate_augur_tree.vcf_reference
File? — Default: None
???

build_augur_tree.translate_augur_tree.vcf_reference_output
File? — Default: None
???

classify_kaiju¶

Inputs¶

Required inputs¶

classify_kaiju.kaiju.kaiju_db_lz4
File — Default: None
???

classify_kaiju.kaiju.krona_taxonomy_db_tgz
File — Default: None
???

classify_kaiju.kaiju.ncbi_taxonomy_db_tgz
File — Default: None
???

classify_kaiju.kaiju.reads_unmapped_bam
File — Default: None
???

Other inputs¶

Show/Hide

classify_kaiju.kaiju.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

classify_kaiju.kaiju.machine_mem_gb
Int? — Default: None
???

classify_krakenuniq¶

Inputs¶

Required inputs¶

classify_krakenuniq.krakenuniq.krakenuniq_db_tar_lz4
File — Default: None
???

classify_krakenuniq.krakenuniq.krona_taxonomy_db_tgz
File — Default: None
???

classify_krakenuniq.krakenuniq.reads_unmapped_bam
Array[File] — Default: None
???

Other inputs¶

Show/Hide

classify_krakenuniq.krakenuniq.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

classify_krakenuniq.krakenuniq.machine_mem_gb
Int? — Default: None
???

classify_krakenuniq.metag_summary_report.aggregate_taxlevel_focus
String — Default: "species"
species,genus,family,order,class,phylum,kingdom,superkingdom

classify_krakenuniq.metag_summary_report.aggregate_taxon_heading_space_separated
String — Default: "Viruses"
The taxonomic heading to analyze. More than one can be specified.

classify_krakenuniq.metag_summary_report.aggregate_top_N_hits
Int? — Default: 5
only include the top N hits from a given sample in the aggregate report

classify_krakenuniq.metag_summary_report.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

contigs¶

Inputs¶

Required inputs¶

contigs.reads_unmapped_bam
File — Default: None
???

contigs.spades.trim_clip_db
File — Default: None
???

Other inputs¶

Show/Hide

contigs.deplete.clear_tags
Boolean? — Default: false
???

contigs.deplete.cpu
Int? — Default: 8
???

contigs.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

contigs.deplete.machine_mem_gb
Int? — Default: None
???

contigs.deplete.query_chunk_size
Int? — Default: None
???

contigs.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

contigs.deplete_blastDbs
Array[File] — Default: []
???

contigs.deplete_bmtaggerDbs
Array[File] — Default: []
???

contigs.deplete_bwaDbs
Array[File] — Default: []
???

contigs.rmdup_ubam.docker
String? — Default: "quay.io/broadinstitute/viral-core"
???

contigs.rmdup_ubam.machine_mem_gb
Int? — Default: None
???

contigs.rmdup_ubam.method
String — Default: "mvicuna"
mvicuna or cdhit

contigs.spades.always_succeed
Boolean? — Default: false
???

contigs.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

contigs.spades.machine_mem_gb
Int? — Default: None
???

contigs.spades.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".taxfilt")
???

contigs.spades.spades_min_contig_len
Int? — Default: 0
???

contigs.spades.spades_n_reads
Int? — Default: 10000000
???

contigs.spades.trinity_n_reads
Int? — Default: 250000
???

coverage_table¶

Inputs¶

Required inputs¶

coverage_table.coverage_report.mapped_bam_idx
Array[File] — Default: None
???

coverage_table.coverage_report.mapped_bams
Array[File]+ — Default: None
???

Other inputs¶

Show/Hide

coverage_table.coverage_report.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

coverage_table.coverage_report.out_report_name
String — Default: "coverage_report.txt"
???

demux_metag¶

Inputs¶

Required inputs¶

demux_metag.illumina_demux.flowcell_tgz
File — Default: None
???

demux_metag.krakenuniq.krakenuniq_db_tar_lz4
File — Default: None
???

demux_metag.krakenuniq.krona_taxonomy_db_tgz
File — Default: None
???

demux_metag.spikein_db
File — Default: None
???

demux_metag.trim_clip_db
File — Default: None
???

Other inputs¶

Show/Hide

demux_metag.blastDbs
Array[File]? — Default: None
???

demux_metag.bmtaggerDbs
Array[File]? — Default: None
???

demux_metag.bwaDbs
Array[File]? — Default: None
???

demux_metag.deplete.clear_tags
Boolean? — Default: false
???

demux_metag.deplete.cpu
Int? — Default: 8
???

demux_metag.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

demux_metag.deplete.machine_mem_gb
Int? — Default: None
???

demux_metag.deplete.query_chunk_size
Int? — Default: None
???

demux_metag.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

demux_metag.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

demux_metag.illumina_demux.flowcell
String? — Default: None
???

demux_metag.illumina_demux.forceGC
Boolean? — Default: true
???

demux_metag.illumina_demux.lane
Int? — Default: 1
???

demux_metag.illumina_demux.machine_mem_gb
Int? — Default: None
???

demux_metag.illumina_demux.maxMismatches
Int? — Default: 0
???

demux_metag.illumina_demux.maxNoCalls
Int? — Default: None
???

demux_metag.illumina_demux.maxReadsInRamPerTile
Int? — Default: None
???

demux_metag.illumina_demux.maxRecordsInRam
Int? — Default: None
???

demux_metag.illumina_demux.minimumBaseQuality
Int? — Default: 10
???

demux_metag.illumina_demux.minimumQuality
Int? — Default: None
???

demux_metag.illumina_demux.minMismatchDelta
Int? — Default: None
???

demux_metag.illumina_demux.readStructure
String? — Default: None
???

demux_metag.illumina_demux.runinfo
File? — Default: None
???

demux_metag.illumina_demux.runStartDate
String? — Default: None
???

demux_metag.illumina_demux.samplesheet
File? — Default: None
???

demux_metag.illumina_demux.sequencingCenter
String? — Default: None
???

demux_metag.illumina_demux.threads
Int? — Default: None
???

demux_metag.krakenuniq.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

demux_metag.krakenuniq.machine_mem_gb
Int? — Default: None
???

demux_metag.metag_summary_report.aggregate_taxlevel_focus
String — Default: "species"
species,genus,family,order,class,phylum,kingdom,superkingdom

demux_metag.metag_summary_report.aggregate_taxon_heading_space_separated
String — Default: "Viruses"
The taxonomic heading to analyze. More than one can be specified.

demux_metag.metag_summary_report.aggregate_top_N_hits
Int? — Default: 5
only include the top N hits from a given sample in the aggregate report

demux_metag.metag_summary_report.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

demux_metag.multiqc_cleaned.comment
String? — Default: None
???

demux_metag.multiqc_cleaned.config
File? — Default: None
???

demux_metag.multiqc_cleaned.config_yaml
String? — Default: None
???

demux_metag.multiqc_cleaned.data_dir
Boolean — Default: false
???

demux_metag.multiqc_cleaned.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

demux_metag.multiqc_cleaned.exclude_modules
Array[String]+? — Default: None
???

demux_metag.multiqc_cleaned.export
Boolean — Default: false
???

demux_metag.multiqc_cleaned.flat
Boolean — Default: false
???

demux_metag.multiqc_cleaned.force
Boolean — Default: false
???

demux_metag.multiqc_cleaned.full_names
Boolean — Default: false
???

demux_metag.multiqc_cleaned.ignore_analysis_files
String? — Default: None
???

demux_metag.multiqc_cleaned.ignore_sample_names
String? — Default: None
???

demux_metag.multiqc_cleaned.interactive
Boolean — Default: true
???

demux_metag.multiqc_cleaned.lint
Boolean — Default: false
???

demux_metag.multiqc_cleaned.megaQC_upload
Boolean — Default: false
???

demux_metag.multiqc_cleaned.module_to_use
Array[String]+? — Default: None
???

demux_metag.multiqc_cleaned.no_data_dir
Boolean — Default: false
???

demux_metag.multiqc_cleaned.out_dir
String — Default: "./multiqc-output"
???

demux_metag.multiqc_cleaned.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_metag.multiqc_cleaned.pdf
Boolean — Default: false
???

demux_metag.multiqc_cleaned.sample_names
File? — Default: None
???

demux_metag.multiqc_cleaned.tag
String? — Default: None
???

demux_metag.multiqc_cleaned.template
String? — Default: None
???

demux_metag.multiqc_cleaned.title
String? — Default: None
???

demux_metag.multiqc_cleaned.zip_data_dir
Boolean — Default: false
???

demux_metag.multiqc_dedup.comment
String? — Default: None
???

demux_metag.multiqc_dedup.config
File? — Default: None
???

demux_metag.multiqc_dedup.config_yaml
String? — Default: None
???

demux_metag.multiqc_dedup.data_dir
Boolean — Default: false
???

demux_metag.multiqc_dedup.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

demux_metag.multiqc_dedup.exclude_modules
Array[String]+? — Default: None
???

demux_metag.multiqc_dedup.export
Boolean — Default: false
???

demux_metag.multiqc_dedup.flat
Boolean — Default: false
???

demux_metag.multiqc_dedup.force
Boolean — Default: false
???

demux_metag.multiqc_dedup.full_names
Boolean — Default: false
???

demux_metag.multiqc_dedup.ignore_analysis_files
String? — Default: None
???

demux_metag.multiqc_dedup.ignore_sample_names
String? — Default: None
???

demux_metag.multiqc_dedup.interactive
Boolean — Default: true
???

demux_metag.multiqc_dedup.lint
Boolean — Default: false
???

demux_metag.multiqc_dedup.megaQC_upload
Boolean — Default: false
???

demux_metag.multiqc_dedup.module_to_use
Array[String]+? — Default: None
???

demux_metag.multiqc_dedup.no_data_dir
Boolean — Default: false
???

demux_metag.multiqc_dedup.out_dir
String — Default: "./multiqc-output"
???

demux_metag.multiqc_dedup.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_metag.multiqc_dedup.pdf
Boolean — Default: false
???

demux_metag.multiqc_dedup.sample_names
File? — Default: None
???

demux_metag.multiqc_dedup.tag
String? — Default: None
???

demux_metag.multiqc_dedup.template
String? — Default: None
???

demux_metag.multiqc_dedup.title
String? — Default: None
???

demux_metag.multiqc_dedup.zip_data_dir
Boolean — Default: false
???

demux_metag.multiqc_raw.comment
String? — Default: None
???

demux_metag.multiqc_raw.config
File? — Default: None
???

demux_metag.multiqc_raw.config_yaml
String? — Default: None
???

demux_metag.multiqc_raw.data_dir
Boolean — Default: false
???

demux_metag.multiqc_raw.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

demux_metag.multiqc_raw.exclude_modules
Array[String]+? — Default: None
???

demux_metag.multiqc_raw.export
Boolean — Default: false
???

demux_metag.multiqc_raw.flat
Boolean — Default: false
???

demux_metag.multiqc_raw.force
Boolean — Default: false
???

demux_metag.multiqc_raw.full_names
Boolean — Default: false
???

demux_metag.multiqc_raw.ignore_analysis_files
String? — Default: None
???

demux_metag.multiqc_raw.ignore_sample_names
String? — Default: None
???

demux_metag.multiqc_raw.interactive
Boolean — Default: true
???

demux_metag.multiqc_raw.lint
Boolean — Default: false
???

demux_metag.multiqc_raw.megaQC_upload
Boolean — Default: false
???

demux_metag.multiqc_raw.module_to_use
Array[String]+? — Default: None
???

demux_metag.multiqc_raw.no_data_dir
Boolean — Default: false
???

demux_metag.multiqc_raw.out_dir
String — Default: "./multiqc-output"
???

demux_metag.multiqc_raw.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_metag.multiqc_raw.pdf
Boolean — Default: false
???

demux_metag.multiqc_raw.sample_names
File? — Default: None
???

demux_metag.multiqc_raw.tag
String? — Default: None
???

demux_metag.multiqc_raw.template
String? — Default: None
???

demux_metag.multiqc_raw.title
String? — Default: None
???

demux_metag.multiqc_raw.zip_data_dir
Boolean — Default: false
???

demux_metag.rmdup_ubam.docker
String? — Default: "quay.io/broadinstitute/viral-core"
???

demux_metag.rmdup_ubam.machine_mem_gb
Int? — Default: None
???

demux_metag.rmdup_ubam.method
String — Default: "mvicuna"
mvicuna or cdhit

demux_metag.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

demux_metag.spades.machine_mem_gb
Int? — Default: None
???

demux_metag.spades.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".taxfilt")
???

demux_metag.spades.spades_min_contig_len
Int? — Default: 0
???

demux_metag.spades.spades_n_reads
Int? — Default: 10000000
???

demux_metag.spades.trinity_n_reads
Int? — Default: 250000
???

demux_metag.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

demux_metag.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

demux_metag.spikein.machine_mem_gb
Int? — Default: None
???

demux_metag.spikein.minScoreToFilter
Int? — Default: 60
???

demux_metag.spikein.topNHits
Int? — Default: 3
???

demux_only¶

Inputs¶

Required inputs¶

demux_only.illumina_demux.flowcell_tgz
File — Default: None
???

Other inputs¶

Show/Hide

demux_only.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

demux_only.illumina_demux.flowcell
String? — Default: None
???

demux_only.illumina_demux.forceGC
Boolean? — Default: true
???

demux_only.illumina_demux.lane
Int? — Default: 1
???

demux_only.illumina_demux.machine_mem_gb
Int? — Default: None
???

demux_only.illumina_demux.maxMismatches
Int? — Default: 0
???

demux_only.illumina_demux.maxNoCalls
Int? — Default: None
???

demux_only.illumina_demux.maxReadsInRamPerTile
Int? — Default: None
???

demux_only.illumina_demux.maxRecordsInRam
Int? — Default: None
???

demux_only.illumina_demux.minimumBaseQuality
Int? — Default: 10
???

demux_only.illumina_demux.minimumQuality
Int? — Default: None
???

demux_only.illumina_demux.minMismatchDelta
Int? — Default: None
???

demux_only.illumina_demux.readStructure
String? — Default: None
???

demux_only.illumina_demux.runinfo
File? — Default: None
???

demux_only.illumina_demux.runStartDate
String? — Default: None
???

demux_only.illumina_demux.samplesheet
File? — Default: None
???

demux_only.illumina_demux.sequencingCenter
String? — Default: None
???

demux_only.illumina_demux.threads
Int? — Default: None
???

demux_only.MultiQC.comment
String? — Default: None
???

demux_only.MultiQC.config
File? — Default: None
???

demux_only.MultiQC.config_yaml
String? — Default: None
???

demux_only.MultiQC.data_dir
Boolean — Default: false
???

demux_only.MultiQC.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

demux_only.MultiQC.exclude_modules
Array[String]+? — Default: None
???

demux_only.MultiQC.export
Boolean — Default: false
???

demux_only.MultiQC.file_name
String? — Default: None
???

demux_only.MultiQC.flat
Boolean — Default: false
???

demux_only.MultiQC.force
Boolean — Default: false
???

demux_only.MultiQC.full_names
Boolean — Default: false
???

demux_only.MultiQC.ignore_analysis_files
String? — Default: None
???

demux_only.MultiQC.ignore_sample_names
String? — Default: None
???

demux_only.MultiQC.interactive
Boolean — Default: true
???

demux_only.MultiQC.lint
Boolean — Default: false
???

demux_only.MultiQC.megaQC_upload
Boolean — Default: false
???

demux_only.MultiQC.module_to_use
Array[String]+? — Default: None
???

demux_only.MultiQC.no_data_dir
Boolean — Default: false
???

demux_only.MultiQC.out_dir
String — Default: "./multiqc-output"
???

demux_only.MultiQC.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_only.MultiQC.pdf
Boolean — Default: false
???

demux_only.MultiQC.sample_names
File? — Default: None
???

demux_only.MultiQC.tag
String? — Default: None
???

demux_only.MultiQC.template
String? — Default: None
???

demux_only.MultiQC.title
String? — Default: None
???

demux_only.MultiQC.zip_data_dir
Boolean — Default: false
???

demux_plus¶

Inputs¶

Required inputs¶

demux_plus.illumina_demux.flowcell_tgz
File — Default: None
???

demux_plus.krakenuniq.krakenuniq_db_tar_lz4
File — Default: None
???

demux_plus.krakenuniq.krona_taxonomy_db_tgz
File — Default: None
???

demux_plus.spikein_db
File — Default: None
???

demux_plus.trim_clip_db
File — Default: None
???

Other inputs¶

Show/Hide

demux_plus.blastDbs
Array[File]? — Default: None
???

demux_plus.bmtaggerDbs
Array[File]? — Default: None
???

demux_plus.bwaDbs
Array[File]? — Default: None
???

demux_plus.deplete.clear_tags
Boolean? — Default: false
???

demux_plus.deplete.cpu
Int? — Default: 8
???

demux_plus.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

demux_plus.deplete.machine_mem_gb
Int? — Default: None
???

demux_plus.deplete.query_chunk_size
Int? — Default: None
???

demux_plus.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

demux_plus.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

demux_plus.illumina_demux.flowcell
String? — Default: None
???

demux_plus.illumina_demux.forceGC
Boolean? — Default: true
???

demux_plus.illumina_demux.lane
Int? — Default: 1
???

demux_plus.illumina_demux.machine_mem_gb
Int? — Default: None
???

demux_plus.illumina_demux.maxMismatches
Int? — Default: 0
???

demux_plus.illumina_demux.maxNoCalls
Int? — Default: None
???

demux_plus.illumina_demux.maxReadsInRamPerTile
Int? — Default: None
???

demux_plus.illumina_demux.maxRecordsInRam
Int? — Default: None
???

demux_plus.illumina_demux.minimumBaseQuality
Int? — Default: 10
???

demux_plus.illumina_demux.minimumQuality
Int? — Default: None
???

demux_plus.illumina_demux.minMismatchDelta
Int? — Default: None
???

demux_plus.illumina_demux.readStructure
String? — Default: None
???

demux_plus.illumina_demux.runinfo
File? — Default: None
???

demux_plus.illumina_demux.runStartDate
String? — Default: None
???

demux_plus.illumina_demux.samplesheet
File? — Default: None
???

demux_plus.illumina_demux.sequencingCenter
String? — Default: None
???

demux_plus.illumina_demux.threads
Int? — Default: None
???

demux_plus.krakenuniq.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

demux_plus.krakenuniq.machine_mem_gb
Int? — Default: None
???

demux_plus.metag_summary_report.aggregate_taxlevel_focus
String — Default: "species"
species,genus,family,order,class,phylum,kingdom,superkingdom

demux_plus.metag_summary_report.aggregate_taxon_heading_space_separated
String — Default: "Viruses"
The taxonomic heading to analyze. More than one can be specified.

demux_plus.metag_summary_report.aggregate_top_N_hits
Int? — Default: 5
only include the top N hits from a given sample in the aggregate report

demux_plus.metag_summary_report.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

demux_plus.multiqc_cleaned.comment
String? — Default: None
???

demux_plus.multiqc_cleaned.config
File? — Default: None
???

demux_plus.multiqc_cleaned.config_yaml
String? — Default: None
???

demux_plus.multiqc_cleaned.data_dir
Boolean — Default: false
???

demux_plus.multiqc_cleaned.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

demux_plus.multiqc_cleaned.exclude_modules
Array[String]+? — Default: None
???

demux_plus.multiqc_cleaned.export
Boolean — Default: false
???

demux_plus.multiqc_cleaned.flat
Boolean — Default: false
???

demux_plus.multiqc_cleaned.force
Boolean — Default: false
???

demux_plus.multiqc_cleaned.full_names
Boolean — Default: false
???

demux_plus.multiqc_cleaned.ignore_analysis_files
String? — Default: None
???

demux_plus.multiqc_cleaned.ignore_sample_names
String? — Default: None
???

demux_plus.multiqc_cleaned.interactive
Boolean — Default: true
???

demux_plus.multiqc_cleaned.lint
Boolean — Default: false
???

demux_plus.multiqc_cleaned.megaQC_upload
Boolean — Default: false
???

demux_plus.multiqc_cleaned.module_to_use
Array[String]+? — Default: None
???

demux_plus.multiqc_cleaned.no_data_dir
Boolean — Default: false
???

demux_plus.multiqc_cleaned.out_dir
String — Default: "./multiqc-output"
???

demux_plus.multiqc_cleaned.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_plus.multiqc_cleaned.pdf
Boolean — Default: false
???

demux_plus.multiqc_cleaned.sample_names
File? — Default: None
???

demux_plus.multiqc_cleaned.tag
String? — Default: None
???

demux_plus.multiqc_cleaned.template
String? — Default: None
???

demux_plus.multiqc_cleaned.title
String? — Default: None
???

demux_plus.multiqc_cleaned.zip_data_dir
Boolean — Default: false
???

demux_plus.multiqc_raw.comment
String? — Default: None
???

demux_plus.multiqc_raw.config
File? — Default: None
???

demux_plus.multiqc_raw.config_yaml
String? — Default: None
???

demux_plus.multiqc_raw.data_dir
Boolean — Default: false
???

demux_plus.multiqc_raw.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

demux_plus.multiqc_raw.exclude_modules
Array[String]+? — Default: None
???

demux_plus.multiqc_raw.export
Boolean — Default: false
???

demux_plus.multiqc_raw.flat
Boolean — Default: false
???

demux_plus.multiqc_raw.force
Boolean — Default: false
???

demux_plus.multiqc_raw.full_names
Boolean — Default: false
???

demux_plus.multiqc_raw.ignore_analysis_files
String? — Default: None
???

demux_plus.multiqc_raw.ignore_sample_names
String? — Default: None
???

demux_plus.multiqc_raw.interactive
Boolean — Default: true
???

demux_plus.multiqc_raw.lint
Boolean — Default: false
???

demux_plus.multiqc_raw.megaQC_upload
Boolean — Default: false
???

demux_plus.multiqc_raw.module_to_use
Array[String]+? — Default: None
???

demux_plus.multiqc_raw.no_data_dir
Boolean — Default: false
???

demux_plus.multiqc_raw.out_dir
String — Default: "./multiqc-output"
???

demux_plus.multiqc_raw.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_plus.multiqc_raw.pdf
Boolean — Default: false
???

demux_plus.multiqc_raw.sample_names
File? — Default: None
???

demux_plus.multiqc_raw.tag
String? — Default: None
???

demux_plus.multiqc_raw.template
String? — Default: None
???

demux_plus.multiqc_raw.title
String? — Default: None
???

demux_plus.multiqc_raw.zip_data_dir
Boolean — Default: false
???

demux_plus.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

demux_plus.spades.machine_mem_gb
Int? — Default: None
???

demux_plus.spades.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".taxfilt")
???

demux_plus.spades.spades_min_contig_len
Int? — Default: 0
???

demux_plus.spades.spades_n_reads
Int? — Default: 10000000
???

demux_plus.spades.trinity_n_reads
Int? — Default: 250000
???

demux_plus.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

demux_plus.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

demux_plus.spikein.machine_mem_gb
Int? — Default: None
???

demux_plus.spikein.minScoreToFilter
Int? — Default: 60
???

demux_plus.spikein.topNHits
Int? — Default: 3
???

deplete_only¶

Inputs¶

Required inputs¶

deplete_only.deplete_taxa.raw_reads_unmapped_bam
File — Default: None
unaligned reads in BAM format

Other inputs¶

Show/Hide

deplete_only.deplete_taxa.blastDbs
Array[File]? — Default: None
Optional list of databases to use for blastn-based depletion. Sequences in fasta format will be indexed on the fly, pre-blast-indexed databases may be provided as tarballs.

deplete_only.deplete_taxa.bmtaggerDbs
Array[File]? — Default: None
Optional list of databases to use for bmtagger-based depletion. Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.

deplete_only.deplete_taxa.bwaDbs
Array[File]? — Default: None
Optional list of databases to use for bwa mem-based depletion. Sequences in fasta format will be indexed on the fly, pre-bwa-indexed databases may be provided as tarballs.

deplete_only.deplete_taxa.clear_tags
Boolean? — Default: false
???

deplete_only.deplete_taxa.cpu
Int? — Default: 8
???

deplete_only.deplete_taxa.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

deplete_only.deplete_taxa.machine_mem_gb
Int? — Default: None
???

deplete_only.deplete_taxa.query_chunk_size
Int? — Default: None
???

deplete_only.deplete_taxa.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

downsample¶

Inputs¶

Required inputs¶

downsample.downsample_bams.reads_bam
Array[File] — Default: None
???

Other inputs¶

Show/Hide

downsample.downsample_bams.deduplicateAfter
Boolean? — Default: false
???

downsample.downsample_bams.deduplicateBefore
Boolean? — Default: false
???

downsample.downsample_bams.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

downsample.downsample_bams.machine_mem_gb
Int? — Default: None
???

downsample.downsample_bams.readCount
Int? — Default: None
???

fastq_to_ubam¶

Inputs¶

Required inputs¶

fastq_to_ubam.FastqToUBAM.fastq_1
File — Default: None
Unaligned read1 file in fastq format

fastq_to_ubam.FastqToUBAM.library_name
String — Default: None
Library name. This is required and will populate the 'LB' read group value. SM & LB combinations must be identical for any sequencing reads generated from the same sequencing library, and must be distinct for any reads generated from different libraries.

fastq_to_ubam.FastqToUBAM.sample_name
String — Default: None
Sample name. This is required and will populate the 'SM' read group value and will be used as the output filename (must be filename-friendly).

Other inputs¶

Show/Hide

fastq_to_ubam.FastqToUBAM.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

fastq_to_ubam.FastqToUBAM.fastq_2
File? — Default: None
Unaligned read2 file in fastq format. This should be empty for single-end read conversion and required for paired-end reads. If provided, it must match fastq_1 in length and order.

fastq_to_ubam.FastqToUBAM.platform_name
String? — Default: None
???

fastq_to_ubam.FastqToUBAM.platform_unit
String? — Default: None
???

fastq_to_ubam.FastqToUBAM.readgroup_name
String? — Default: None
???

fastq_to_ubam.FastqToUBAM.run_date
String? — Default: None
???

fastq_to_ubam.FastqToUBAM.sequencing_center
String? — Default: None
???

fetch_annotations¶

Inputs¶

Required inputs¶

fetch_annotations.download_annotations.accessions
Array[String]+ — Default: None
???

fetch_annotations.download_annotations.combined_out_prefix
String — Default: None
???

fetch_annotations.download_annotations.emailAddress
String — Default: None
???

Other inputs¶

Show/Hide

fetch_annotations.download_annotations.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

fetch_annotations.download_annotations.machine_mem_gb
Int? — Default: None
???

multi_Fetch_SRA_to_BAM¶

Inputs¶

Required inputs¶

multi_Fetch_SRA_to_BAM.SRR_accessions
Array[String] — Default: None
???

Other inputs¶

Show/Hide

multi_Fetch_SRA_to_BAM.Fetch_SRA_to_BAM.docker
String — Default: "quay.io/broadinstitute/ncbi-tools"
???

multi_Fetch_SRA_to_BAM.Fetch_SRA_to_BAM.machine_mem_gb
Int? — Default: None
???

filter_classified_bam_to_taxa¶

Inputs¶

Required inputs¶

filter_classified_bam_to_taxa.filter_bam_to_taxa.classified_bam
File — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.classified_reads_txt_gz
File — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.ncbi_taxonomy_db_tgz
File — Default: None
???

Other inputs¶

Show/Hide

filter_classified_bam_to_taxa.filter_bam_to_taxa.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.machine_mem_gb
Int? — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.taxonomic_ids
Array[Int]? — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.taxonomic_names
Array[String]? — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.withoutChildren
Boolean? — Default: false
???

genbank¶

Inputs¶

Required inputs¶

genbank.annot.reference_feature_table
Array[File]+ — Default: None
tbl; feature table corresponding to each chromosome in the alignment

genbank.assemblies_fasta
Array[File]+ — Default: None
???

genbank.prep_genbank.authors_sbt
File — Default: None
???

genbank.prep_genbank.biosampleMap
File — Default: None
???

genbank.prep_genbank.comment
String — Default: None
???

genbank.prep_genbank.genbankSourceTable
File — Default: None
???

genbank.prep_genbank.organism
String — Default: None
???

genbank.prep_genbank.sequencingTech
String — Default: None
???

genbank.reference_fasta
File — Default: None
???

Other inputs¶

Show/Hide

genbank.annot.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

genbank.annot.machine_mem_gb
Int? — Default: None
???

genbank.mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

genbank.mafft.fasta_basename
String — Default: basename(reference_fasta,'.fasta')
???

genbank.mafft.machine_mem_gb
Int? — Default: None
???

genbank.mafft.mafft_ep
Float? — Default: None
???

genbank.mafft.mafft_gapOpeningPenalty
Float? — Default: None
???

genbank.mafft.mafft_maxIters
Int? — Default: None
???

genbank.prep_genbank.coverage_table
File? — Default: None
???

genbank.prep_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

genbank.prep_genbank.machine_mem_gb
Int? — Default: None
???

genbank.prep_genbank.molType
String — Default: "cRNA"
???

isnvs_merge_to_vcf¶

Inputs¶

Required inputs¶

isnvs_merge_to_vcf.assemblies_fasta
Array[File]+ — Default: None
???

isnvs_merge_to_vcf.isnvs_vcf.vphaser2Calls
Array[File] — Default: None
vphaser output; ex. vphaser2..txt.gz

isnvs_merge_to_vcf.reference_fasta
File — Default: None
???

Other inputs¶

Show/Hide

isnvs_merge_to_vcf.isnvs_vcf.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

isnvs_merge_to_vcf.isnvs_vcf.emailAddress
String? — Default: None
email address passed to NCBI if we need to download reference sequences

isnvs_merge_to_vcf.isnvs_vcf.machine_mem_gb
Int? — Default: None
???

isnvs_merge_to_vcf.isnvs_vcf.naiveFilter
Boolean — Default: false
???

isnvs_merge_to_vcf.isnvs_vcf.sampleNames
Array[String]? — Default: None
list of sample names

isnvs_merge_to_vcf.isnvs_vcf.snpEffRef
Array[String]? — Default: None
list of accessions to build/find snpEff database

isnvs_merge_to_vcf.mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

isnvs_merge_to_vcf.mafft.fasta_basename
String — Default: basename(reference_fasta,'.fasta')
???

isnvs_merge_to_vcf.mafft.machine_mem_gb
Int? — Default: None
???

isnvs_merge_to_vcf.mafft.mafft_ep
Float? — Default: None
???

isnvs_merge_to_vcf.mafft.mafft_gapOpeningPenalty
Float? — Default: None
???

isnvs_merge_to_vcf.mafft.mafft_maxIters
Int? — Default: None
???

isnvs_one_sample¶

Inputs¶

Required inputs¶

isnvs_one_sample.isnvs_per_sample.assembly_fasta
File — Default: None
???

isnvs_one_sample.isnvs_per_sample.mapped_bam
File — Default: None
???

Other inputs¶

Show/Hide

isnvs_one_sample.isnvs_per_sample.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

isnvs_one_sample.isnvs_per_sample.machine_mem_gb
Int? — Default: None
???

isnvs_one_sample.isnvs_per_sample.maxBias
Int? — Default: None
???

isnvs_one_sample.isnvs_per_sample.minReadsPerStrand
Int? — Default: None
???

isnvs_one_sample.isnvs_per_sample.sample_name
String — Default: basename(basename(basename(mapped_bam,".bam"),".all"),".mapped")
???

isnvs_one_sample.isnvs_per_sample.threads
Int? — Default: None
???

mafft¶

Inputs¶

Required inputs¶

mafft.multi_align_mafft.assemblies_fasta
Array[File]+ — Default: None
???

Other inputs¶

Show/Hide

mafft.multi_align_mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

mafft.multi_align_mafft.machine_mem_gb
Int? — Default: None
???

mafft.multi_align_mafft.mafft_ep
Float? — Default: None
???

mafft.multi_align_mafft.mafft_gapOpeningPenalty
Float? — Default: None
???

mafft.multi_align_mafft.mafft_maxIters
Int? — Default: None
???

mafft.multi_align_mafft.out_prefix
String — Default: "aligned"
???

mafft_and_trim¶

Inputs¶

Required inputs¶

mafft_and_trim.mafft.assemblies_fasta
Array[File]+ — Default: None
???

Other inputs¶

Show/Hide

mafft_and_trim.mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo"
???

mafft_and_trim.mafft.machine_mem_gb
Int? — Default: None
???

mafft_and_trim.mafft.mafft_ep
Float? — Default: None
???

mafft_and_trim.mafft.mafft_gapOpeningPenalty
Float? — Default: None
???

mafft_and_trim.mafft.mafft_maxIters
Int? — Default: None
???

mafft_and_trim.mafft.out_prefix
String — Default: "aligned"
???

mafft_and_trim.trimal.docker
String — Default: "quay.io/biocontainers/trimal:1.4.1--h6bb024c_3"
???

mafft_and_trim.trimal.input_basename
String — Default: basename(basename(in_aligned_fasta,".fasta"),".fa")
???

mafft_and_trim.trimal.machine_mem_gb
Int? — Default: None
???

merge_bams¶

Inputs¶

Required inputs¶

merge_bams.merge_and_reheader_bams.in_bams
Array[File]+ — Default: None
???

merge_bams.merge_and_reheader_bams.out_basename
String — Default: None
???

Other inputs¶

Show/Hide

merge_bams.merge_and_reheader_bams.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

merge_bams.merge_and_reheader_bams.reheader_table
File? — Default: None
???

merge_bams.merge_and_reheader_bams.sample_name
String? — Default: None
???

merge_metagenomics¶

Inputs¶

Required inputs¶

merge_metagenomics.krakenuniq_summary_reports
Array[File] — Default: None
???

merge_metagenomics.krona_per_sample
Array[File] — Default: None
???

Other inputs¶

Show/Hide

merge_metagenomics.aggregate_metagenomics_reports.aggregate_taxlevel_focus
String — Default: "species"
species,genus,family,order,class,phylum,kingdom,superkingdom

merge_metagenomics.aggregate_metagenomics_reports.aggregate_taxon_heading_space_separated
String — Default: "Viruses"
The taxonomic heading to analyze. More than one can be specified.

merge_metagenomics.aggregate_metagenomics_reports.aggregate_top_N_hits
Int? — Default: 5
only include the top N hits from a given sample in the aggregate report

merge_metagenomics.aggregate_metagenomics_reports.docker
String — Default: "quay.io/broadinstitute/viral-classify"
???

merge_metagenomics.krona_merge.docker
String — Default: "biocontainers/krona:v2.7.1_cv1"
???

merge_metagenomics.krona_merge.machine_mem_gb
Int? — Default: None
???

merge_tar_chunks¶

Inputs¶

Required inputs¶

merge_tar_chunks.merge_tarballs.out_filename
String — Default: None
???

merge_tar_chunks.merge_tarballs.tar_chunks
Array[File]+ — Default: None
???

Other inputs¶

Show/Hide

merge_tar_chunks.merge_tarballs.docker
String — Default: "quay.io/broadinstitute/viral-core"
???

merge_tar_chunks.merge_tarballs.machine_mem_gb
Int? — Default: None
???

multiqc_only¶

Inputs¶

Other inputs¶

Show/Hide

multiqc_only.MultiQC.comment
String? — Default: None
???

multiqc_only.MultiQC.config
File? — Default: None
???

multiqc_only.MultiQC.config_yaml
String? — Default: None
???

multiqc_only.MultiQC.data_dir
Boolean — Default: false
???

multiqc_only.MultiQC.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

multiqc_only.MultiQC.exclude_modules
Array[String]+? — Default: None
???

multiqc_only.MultiQC.export
Boolean — Default: false
???

multiqc_only.MultiQC.file_name
String? — Default: None
???

multiqc_only.MultiQC.flat
Boolean — Default: false
???

multiqc_only.MultiQC.force
Boolean — Default: false
???

multiqc_only.MultiQC.full_names
Boolean — Default: false
???

multiqc_only.MultiQC.ignore_analysis_files
String? — Default: None
???

multiqc_only.MultiQC.ignore_sample_names
String? — Default: None
???

multiqc_only.MultiQC.input_files
Array[File] — Default: []
???

multiqc_only.MultiQC.interactive
Boolean — Default: true
???

multiqc_only.MultiQC.lint
Boolean — Default: false
???

multiqc_only.MultiQC.megaQC_upload
Boolean — Default: false
???

multiqc_only.MultiQC.module_to_use
Array[String]+? — Default: None
???

multiqc_only.MultiQC.no_data_dir
Boolean — Default: false
???

multiqc_only.MultiQC.out_dir
String — Default: "./multiqc-output"
???

multiqc_only.MultiQC.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

multiqc_only.MultiQC.pdf
Boolean — Default: false
???

multiqc_only.MultiQC.sample_names
File? — Default: None
???

multiqc_only.MultiQC.tag
String? — Default: None
???

multiqc_only.MultiQC.template
String? — Default: None
???

multiqc_only.MultiQC.title
String? — Default: None
???

multiqc_only.MultiQC.zip_data_dir
Boolean — Default: false
???

scaffold_and_refine¶

Inputs¶

Required inputs¶

scaffold_and_refine.reads_unmapped_bam
File — Default: None
???

scaffold_and_refine.scaffold.contigs_fasta
File — Default: None
???

scaffold_and_refine.scaffold.reference_genome_fasta
Array[File]+ — Default: None
???

Other inputs¶

Show/Hide

scaffold_and_refine.refine_2x_and_plot.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

scaffold_and_refine.refine_2x_and_plot.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.refine_2x_and_plot.novocraft_license
File? — Default: None
???

scaffold_and_refine.refine_2x_and_plot.plot_coverage_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100 -k"
???

scaffold_and_refine.refine_2x_and_plot.refine1_major_cutoff
Float? — Default: 0.5
???

scaffold_and_refine.refine_2x_and_plot.refine1_min_coverage
Int? — Default: 2
???

scaffold_and_refine.refine_2x_and_plot.refine1_novoalign_options
String? — Default: "-r Random -l 30 -g 40 -x 20 -t 502"
???

scaffold_and_refine.refine_2x_and_plot.refine2_major_cutoff
Float? — Default: 0.5
???

scaffold_and_refine.refine_2x_and_plot.refine2_min_coverage
Int? — Default: 3
???

scaffold_and_refine.refine_2x_and_plot.refine2_novoalign_options
String? — Default: "-r Random -l 40 -g 40 -x 20 -t 100"
???

scaffold_and_refine.refine_2x_and_plot.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".cleaned")
???

scaffold_and_refine.scaffold.aligner
String? — Default: None
???

scaffold_and_refine.scaffold.docker
String — Default: "quay.io/broadinstitute/viral-assemble"
???

scaffold_and_refine.scaffold.machine_mem_gb
Int? — Default: None
???

scaffold_and_refine.scaffold.min_length_fraction
Float? — Default: None
???

scaffold_and_refine.scaffold.min_unambig
Float? — Default: None
???

scaffold_and_refine.scaffold.nucmer_max_gap
Int? — Default: None
???

scaffold_and_refine.scaffold.nucmer_min_cluster
Int? — Default: None
???

scaffold_and_refine.scaffold.nucmer_min_match
Int? — Default: None
???

scaffold_and_refine.scaffold.replace_length
Int? — Default: 55
???

scaffold_and_refine.scaffold.sample_name
String — Default: basename(basename(basename(contigs_fasta,".fasta"),".assembly1-trinity"),".assembly1-spades")
???

scaffold_and_refine.scaffold.scaffold_min_pct_contig_aligned
Float? — Default: None
???

trimal¶

Inputs¶

Required inputs¶

trimal.trimal_clean_msa.in_aligned_fasta
File — Default: None
???

Other inputs¶

Show/Hide

trimal.trimal_clean_msa.docker
String — Default: "quay.io/biocontainers/trimal:1.4.1--h6bb024c_3"
???

trimal.trimal_clean_msa.input_basename
String — Default: basename(basename(in_aligned_fasta,".fasta"),".fa")
???

trimal.trimal_clean_msa.machine_mem_gb
Int? — Default: None
???