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 SPAdes. 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.

Submitting viral sequences to NCBI¶

Register your BioProject¶

If you want to add samples to an existing BioProject, skip to Step 2.

Go to: https://submit.ncbi.nlm.nih.gov and login (new users - create new login).
Go to the Submissions tab and select BioProject - click on New Submission.
Follow the onscreen instructions and then click submit - you will receive a BioProject ID (PRJNA###) via email almost immediately.

Register your BioSamples¶

Go to: https://submit.ncbi.nlm.nih.gov and login.
Go to the Submissions tab and select BioSample - click on New Submission.
Follow instructions, selecting “batch submission type” where applicable.
The metadata template to use is likely: “Pathogen affecting public health” (Pathogen.cl.1.0.xlsx).
Follow template instructions to fill in the sheet. Pay particular attention to the Excel comments that are attached to each column header: they describe the intended content for these columns, the valid formatting, and controlled vocabulary.
1. For example, “organism” should always match the long name that is given by the NCBI Taxonomy database for that species.
2. Date fields seem to have multiple acceptable formats, but we prefer ISO8601 (YYYY-MM-DD) just to reduce ambiguity. Note that this format will trigger a warning when uploading, if you don’t have HH:MM time values as well (it will suggest an edit for you).
3. You will likely need to duplicate your sample_name to the host_subject_id column (or something like it)–if you do not, then any samples that happen to have the same attribute values will trigger an error when trying to register new BioSamples because they look like duplicates. Assuming that your sample_names are one-to-one corresponding to a human patient, host_subject_id is probably the most appropriate place to duplicate the value in order to make all entries unique.
4. Populate the isolate column using the naming convention you want to apply to this organism (most viral species have a specific, structured naming convention you should follow). Our workflow will re-use this value for the Genbank record name.
Export to text and submit as .txt file. You will receive BioSamples IDs (SAMN####) via email (often 1-2 days later).
After NCBI accepts your submission and registers your samples, retrieve the text-formatted “attributes table” associated with this submission from the portal at https://submit.ncbi.nlm.nih.gov/subs/ and clicking on “Download attributes file with BioSample accessions”. You will need this file later. Do not use the file that was attached to the NCBI response email–it does not contain the full record and is formatted differently.
If you wish to amend/correct any metadata in your submissions, you can always do so at a future time – however, you will need BioSample IDs before any of the following steps, so it’s best to register as soon as you have collection_date and sample_name for everything. This can be a super-set of anything you submit to NCBI in the future (Genbank or SRA), so we typically register BioSamples for every viral sample we attempt to sequence, regardless of whether we successfully sequenced it or not.

Set up an NCBI author template¶

If different author lists are used for different sets of samples, create a new .sbt file for each list

Go to: https://submit.ncbi.nlm.nih.gov/genbank/template/submission/
Fill out the form including all authors and submitter information (if unpublished, the reference title can be just a general description of the project).
At the end of the form, include the BioProject number from Step 1 but NOT the BioSample number’
Click “create template” which will download an .sbt file to your computer’
Save file as “authors.sbt” or similar. If you have multiple author files, give each file a different name and prep your submissions as separate batches, one for each authors.sbt file.

Prepare requisite input files for your submission batches¶

Stage the above files you’ve prepared and other requisite inputs into the environment you plan to execute the genbank WDL workflow. If that is Terra, push these files into the appropriate GCS bucket, if DNAnexus, drop your files there. If you plan to execute locally (e.g. with miniwdl run), move the files to an appropriate directory on your machine. The files you will need are the following:
1. The files you prepared above: the submission template (authors.sbt) and the biosample attributes table (attributes.tsv).
2. All of the assemblies you want to submit. These should be in fasta files, one per genome. Multi-segment/multi-chromosome genomes (such as Lassa virus, Influenza A, etc) should contain all segments within one fasta file.
3. Your reference genome, as a set of fasta files, one per segment/chromosome. The fasta sequence headers should be Genbank accession numbers. This can come directly from Genbank.
4. Your reference gene annotations, as a set of TBL files, one per segment/chromosome. These must correspond to the accessions in your reference genome. These must be presented in the same order as the reference genome fasta files, which must also be in the same order as all the sequences in all of your assembled fasta files.
5. A genome coverage table as a two-column tabular text file (optional, but helpful).
6. The organism name (which should match what NCBI taxonomy calls the species you are submitting for). This is a string input to the workflow, not a file.
7. The sequencing technology used. This is a string input, not a file.
8. The NCBI Taxonomy taxid. This is a numeric input, not a file.
The reference genome you provide should be annotated in the way you want your genomes annotated on NCBI. If one doesn’t exist, see the addendum below about creating your own feature list.
Note that you will have to run the pipeline separately for each virus you are submitting AND separately for each author list.

Run the genbank submission pipeline¶

Run the genbank WDL workflow. Most of the metadata files described above (BioSample map, source modifier table, genome coverage table) are allowed to be a super-set of the samples you are submitting–the extra metadata will be ignored by the workflow. The samples that are included in this batch are the ones you provide to the assemblies_fasta input field. Any missing samples in the metadata inputs should not cause failures, but will produce less descriptive submission files. Viral genomes should set molType to cRNA.
The genbank workflow performs the following steps: it aligns your assemblies against a Genbank reference sequence, transfers gene annotation from that Genbank reference into your assemblies’ coordinate spaces, and then takes your genomes, the transferred annotations, and all of the sample metadata prepared above, and produces a zipped bundle that you send to NCBI. There are two zip bundles: sequins_only.zip is the file to email to NCBI. all_files.zip contains a full set of files for your inspection prior to submission.
In the all_files.zip output, for each sample, you will see a .sqn, .gbf, .val, and .tbl file. You should also see an errorsummary.val file that you can use to check for annotation errors (or you can check the .val file for each sample individually). Ideally, your samples should be error-free before you submit them to NCBI unless you’re confident enough in the genomic evidence for unusual coding effects and frameshifts. For an explanation of the cryptic error messages, see: https://www.ncbi.nlm.nih.gov/genbank/genome_validation/.
We currently use a bioconda wrapper of NCBI’s tbl2asn tool called tbl2asn-forever. This works around some deficiencies in NCBI’s tool but has the side effect of setting the submission date to Jan 1, 2019 for all submission, regardless of today’s date. Unfortunately, until NCBI releases a fixed tool, you will need to search-replace the date in the SQN files in a text editor prior to submission.
Check your .gbf files for a preview of what your genbank entries will look like. Once you are happy with your files email the sequins_only.zip file to gb-sub@ncbi.nlm.nih.gov.
It often takes 2-8 weeks to receive a response and accession numbers for your samples. Do follow up if you haven’t heard anything for a few weeks!

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¶

Align reads to reference with minimap2 and count the number of hits. Results are returned in the format of ‘samtools idxstats’.

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¶

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align_and_count_report.align_and_count.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

align_and_count_multiple_report¶

Count the number of times reads map to provided reference sequences. Useful for counting spike-ins, etc.

Inputs¶

Required inputs¶

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

align_and_count_multiple_report.ref_db
File — Default: None
File containing sequences against which reads should me aligned and counted

Other inputs¶

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align_and_count_multiple_report.align_and_count.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

align_and_count_multiple_report.align_and_count_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

align_and_count_multiple_report.align_and_count_summary.output_prefix
String — Default: "count_summary"
???

align_and_count_multiple_report.align_and_count_summary_top_hits.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

align_and_plot¶

Align reads to reference and produce coverage plots and statistics.

Inputs¶

Required inputs¶

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

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

Other inputs¶

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align_and_plot.align.aligner
String — Default: "minimap2"
Short read aligner to use: novoalign, minimap2, or bwa. (Default: novoalign)

align_and_plot.align.aligner_options
String? — Default: None
???

align_and_plot.align.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

align_and_plot.align.machine_mem_gb
Int? — Default: None
???

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.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:2.1.19"
???

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¶

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assemble_denovo.assemble.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

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.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:2.1.16.0"
???

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:2.1.16.0"
???

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:2.1.16.0"
???

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.removeDoublyMappedReads
Boolean — Default: true
???

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:2.1.16.1"
???

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:2.1.19"
???

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:2.1.16.1"
???

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

assemble_denovo.scaffold.sample_name
String — Default: basename(basename(contigs_fasta,".fasta"),".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 NGS 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.

Other common inputs¶

assemble_refbased.sample_name
String — Default: basename(reads_unmapped_bams[0],'.bam')
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.

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

Other inputs¶

Show/Hide

assemble_refbased.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

assemble_refbased.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

assemble_refbased.aligner
String — Default: "minimap2"
Read aligner software to use. Options: novoalign, bwa, minimap2. Minimap2 can automatically handle Illumina, PacBio, or Oxford Nanopore reads as long as the 'PL' field in the BAM read group header is set properly (novoalign and bwa are Illumina-only).

assemble_refbased.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

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

assemble_refbased.call_consensus.major_cutoff
Float? — Default: 0.5
If the major allele is present at a frequency higher than this cutoff, we will call an unambiguous base at that position. If it is equal to or below this cutoff, we will call an ambiguous base representing all possible alleles at that position.

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

assemble_refbased.ivar_trim.docker
String — Default: "andersenlabapps/ivar:1.3"
???

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: 1
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:2.1.19"
???

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:2.1.19"
???

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

assemble_refbased.min_coverage
Int — Default: 3
Minimum read coverage required to call a position unambiguous.

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:2.1.19"
???

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:2.1.19"
???

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.run_discordance.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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)

augur_export_only¶

Convert a newick formatted phylogenetic tree with other config settings and node values into a json suitable for auspice visualization. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/export.html

Inputs¶

Required inputs¶

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

augur_export_only.export_auspice_json.node_data_jsons
Array[File] — Default: None
???

augur_export_only.export_auspice_json.tree
File — Default: None
???

Other inputs¶

Show/Hide

augur_export_only.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???

augur_export_only.export_auspice_json.colors_tsv
File? — Default: None
???

augur_export_only.export_auspice_json.description_md
File? — Default: None
???

augur_export_only.export_auspice_json.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_export_only.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???

augur_export_only.export_auspice_json.lat_longs_tsv
File? — Default: None
???

augur_export_only.export_auspice_json.maintainers
Array[String]? — Default: None
???

augur_export_only.export_auspice_json.sample_metadata
File? — Default: None
???

augur_export_only.export_auspice_json.title
String? — Default: None
???

augur_from_assemblies¶

Align assemblies, build trees, and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/

Inputs¶

Required inputs¶

augur_from_assemblies.assembly_fastas
Array[File]+ — Default: None
Set of assembled genomes to align and build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.

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

augur_from_assemblies.min_unambig_genome
Int — Default: None
Minimum number of called bases in genome to pass prefilter.

augur_from_assemblies.ref_fasta
File — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar.

augur_from_assemblies.sample_metadata_tsvs
Array[File]+ — Default: None
Tab-separated metadata file that contain binning variables and values. Must contain all samples: output will be filtered to the IDs present in this file.

augur_from_assemblies.translate_augur_tree.genbank_gb
File — Default: None
???

Other inputs¶

Show/Hide

augur_from_assemblies.ancestral_traits.confidence
Boolean — Default: true
???

augur_from_assemblies.ancestral_traits.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_assemblies.ancestral_traits.sampling_bias_correction
Float? — Default: None
???

augur_from_assemblies.ancestral_traits.weights
File? — Default: None
???

augur_from_assemblies.ancestral_traits_to_infer
Array[String]? — Default: None
A list of metadata traits to use for ancestral node inference (see https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/traits.html). Multiple traits may be specified; must correspond exactly to column headers in metadata file. Omitting these values will skip ancestral trait inference, and ancestral nodes will not have estimated values for metadata.

augur_from_assemblies.ancestral_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

augur_from_assemblies.ancestral_tree.inference
String — Default: "joint"
???

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

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

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

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

augur_from_assemblies.assign_clades_to_nodes.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_assemblies.augur_mask_sites.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_assemblies.augur_mask_sites.mask_bed
File? — Default: None
???

augur_from_assemblies.clades_tsv
File? — Default: None
A TSV file containing clade mutation positions in four columns: [clade gene site alt]; see: https://nextstrain.org/docs/tutorials/defining-clades

augur_from_assemblies.derived_cols.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

augur_from_assemblies.derived_cols.lab_highlight_loc
String? — Default: None
???

augur_from_assemblies.derived_cols.table_map
Array[File] — Default: []
???

augur_from_assemblies.draft_augur_tree.cpus
Int? — Default: None
???

augur_from_assemblies.draft_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

augur_from_assemblies.draft_augur_tree.method
String — Default: "iqtree"
???

augur_from_assemblies.draft_augur_tree.substitution_model
String — Default: "GTR"
???

augur_from_assemblies.draft_augur_tree.tree_builder_args
String? — Default: None
???

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

augur_from_assemblies.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???

augur_from_assemblies.export_auspice_json.colors_tsv
File? — Default: None
???

augur_from_assemblies.export_auspice_json.description_md
File? — Default: None
???

augur_from_assemblies.export_auspice_json.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_assemblies.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???

augur_from_assemblies.export_auspice_json.lat_longs_tsv
File? — Default: None
???

augur_from_assemblies.export_auspice_json.maintainers
Array[String]? — Default: None
???

augur_from_assemblies.export_auspice_json.title
String? — Default: None
???

augur_from_assemblies.filter_sequences_by_length.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

augur_from_assemblies.focal_bin_max
Int — Default: 50
The output will contain no more than this number of focal samples from each discrete value in the focal_bin_variable column.

augur_from_assemblies.focal_bin_variable
String — Default: "division"
The focal subset of samples will be evenly subsampled across the discrete values of this column header.

augur_from_assemblies.focal_value
String — Default: "North America"
The dataset will be bifurcated based whether the focal_variable column matches this value or not. Rows that match this value are considered to be part of the 'focal' set of interest, rows that do not are part of the 'global' set.

augur_from_assemblies.focal_variable
String — Default: "region"
The dataset will be bifurcated based on this column header.

augur_from_assemblies.global_bin_max
Int — Default: 50
The output will contain no more than this number of global samples from each discrete value in the global_bin_variable column.

augur_from_assemblies.global_bin_variable
String — Default: "country"
The global subset of samples will be evenly subsampled across the discrete values of this column header.

augur_from_assemblies.gzcat.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

augur_from_assemblies.mafft.cpus
Int — Default: 32
???

augur_from_assemblies.mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

augur_from_assemblies.mafft.keep_length
Boolean — Default: true
???

augur_from_assemblies.mafft.large
Boolean — Default: false
???

augur_from_assemblies.mafft.mem_size
Int — Default: 250
???

augur_from_assemblies.mafft.memsavetree
Boolean — Default: false
???

augur_from_assemblies.mafft.remove_reference
Boolean — Default: false
???

augur_from_assemblies.prefilter.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_assemblies.prefilter.exclude
File? — Default: None
???

augur_from_assemblies.prefilter.exclude_where
Array[String]? — Default: None
???

augur_from_assemblies.prefilter.group_by
String? — Default: None
???

augur_from_assemblies.prefilter.include
File? — Default: None
???

augur_from_assemblies.prefilter.include_where
Array[String]? — Default: None
???

augur_from_assemblies.prefilter.max_date
Float? — Default: None
???

augur_from_assemblies.prefilter.min_date
Float? — Default: None
???

augur_from_assemblies.prefilter.min_length
Int? — Default: None
???

augur_from_assemblies.prefilter.non_nucleotide
Boolean — Default: true
???

augur_from_assemblies.prefilter.priority
File? — Default: None
???

augur_from_assemblies.prefilter.sequences_per_group
Int? — Default: None
???

augur_from_assemblies.prefilter.subsample_seed
Int? — Default: None
???

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

augur_from_assemblies.refine_augur_tree.clock_filter_iqd
Int? — Default: 4
???

augur_from_assemblies.refine_augur_tree.clock_rate
Float? — Default: None
???

augur_from_assemblies.refine_augur_tree.clock_std_dev
Float? — Default: None
???

augur_from_assemblies.refine_augur_tree.coalescent
String? — Default: None
???

augur_from_assemblies.refine_augur_tree.covariance
Boolean? — Default: None
???

augur_from_assemblies.refine_augur_tree.date_confidence
Boolean — Default: true
???

augur_from_assemblies.refine_augur_tree.date_inference
String? — Default: "marginal"
???

augur_from_assemblies.refine_augur_tree.divergence_units
String? — Default: "mutations"
???

augur_from_assemblies.refine_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

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

augur_from_assemblies.refine_augur_tree.keep_root
Boolean — Default: true
???

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

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

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

augur_from_assemblies.snp_sites.allow_wildcard_bases
Boolean — Default: true
???

augur_from_assemblies.snp_sites.docker
String — Default: "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
???

augur_from_assemblies.subsample_focal.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_assemblies.subsample_focal.exclude
File? — Default: None
???

augur_from_assemblies.subsample_focal.include
File? — Default: None
???

augur_from_assemblies.subsample_focal.include_where
Array[String]? — Default: None
???

augur_from_assemblies.subsample_focal.max_date
Float? — Default: None
???

augur_from_assemblies.subsample_focal.min_date
Float? — Default: None
???

augur_from_assemblies.subsample_focal.min_length
Int? — Default: None
???

augur_from_assemblies.subsample_focal.non_nucleotide
Boolean — Default: true
???

augur_from_assemblies.subsample_focal.priority
File? — Default: None
???

augur_from_assemblies.subsample_focal.subsample_seed
Int? — Default: None
???

augur_from_assemblies.subsample_global.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_assemblies.subsample_global.exclude
File? — Default: None
???

augur_from_assemblies.subsample_global.include
File? — Default: None
???

augur_from_assemblies.subsample_global.include_where
Array[String]? — Default: None
???

augur_from_assemblies.subsample_global.max_date
Float? — Default: None
???

augur_from_assemblies.subsample_global.min_date
Float? — Default: None
???

augur_from_assemblies.subsample_global.min_length
Int? — Default: None
???

augur_from_assemblies.subsample_global.non_nucleotide
Boolean — Default: true
???

augur_from_assemblies.subsample_global.priority
File? — Default: None
???

augur_from_assemblies.subsample_global.subsample_seed
Int? — Default: None
???

augur_from_assemblies.translate_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

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

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

augur_from_assemblies.tsv_join.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

augur_from_beast_mcc¶

Visualize BEAST output with Nextstrain. This workflow converts a BEAST MCC tree (.tree file) into an Auspice v2 json file. See https://nextstrain-augur.readthedocs.io/en/stable/faq/import-beast.html for details.

Inputs¶

Required inputs¶

augur_from_beast_mcc.auspice_config
File — Default: None
A file specifying options to customize the auspice export; see: https://nextstrain.github.io/auspice/customise-client/introduction

augur_from_beast_mcc.beast_mcc_tree
File — Default: None
A maximum clade credibility (MCC) tree (.tree file) that is output from a BEAST run.

Other inputs¶

Show/Hide

augur_from_beast_mcc.augur_import_beast.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_beast_mcc.augur_import_beast.machine_mem_gb
Int? — Default: None
???

augur_from_beast_mcc.augur_import_beast.most_recent_tip_date
Float? — Default: None
???

augur_from_beast_mcc.augur_import_beast.tip_date_delimiter
String? — Default: None
???

augur_from_beast_mcc.augur_import_beast.tip_date_format
String? — Default: None
???

augur_from_beast_mcc.augur_import_beast.tip_date_regex
String? — Default: None
???

augur_from_beast_mcc.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???

augur_from_beast_mcc.export_auspice_json.colors_tsv
File? — Default: None
???

augur_from_beast_mcc.export_auspice_json.description_md
File? — Default: None
???

augur_from_beast_mcc.export_auspice_json.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_beast_mcc.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???

augur_from_beast_mcc.export_auspice_json.lat_longs_tsv
File? — Default: None
???

augur_from_beast_mcc.export_auspice_json.maintainers
Array[String]? — Default: None
???

augur_from_beast_mcc.export_auspice_json.sample_metadata
File? — Default: None
???

augur_from_beast_mcc.export_auspice_json.title
String? — Default: None
???

augur_from_mltree¶

Take a premade maximum likelihood tree (Newick format) and run the remainder of the augur pipeline (timetree modificaitons, ancestral inference, etc) and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/

Inputs¶

Required inputs¶

augur_from_mltree.auspice_config
File — Default: None
A file specifying options to customize the auspice export; see: https://nextstrain.github.io/auspice/customise-client/introduction

augur_from_mltree.genbank_gb
File — Default: None
A 'genbank' formatted gene annotation file that is used to calculate coding consequences of observed mutations. Must correspond to the same coordinate space as ref_fasta. Typically downloaded from the same NCBI accession number as ref_fasta.

augur_from_mltree.msa_or_vcf
File — Default: None
Multiple sequence alignment (aligned fasta) or variants (vcf format).

augur_from_mltree.raw_tree
File — Default: None
Maximum likelihood tree (newick format).

augur_from_mltree.ref_fasta
File — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar.

augur_from_mltree.sample_metadata
File — Default: None
Metadata in tab-separated text format. See https://nextstrain-augur.readthedocs.io/en/stable/faq/metadata.html for details.

Other inputs¶

Show/Hide

augur_from_mltree.ancestral_traits.confidence
Boolean — Default: true
???

augur_from_mltree.ancestral_traits.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_mltree.ancestral_traits.sampling_bias_correction
Float? — Default: None
???

augur_from_mltree.ancestral_traits.weights
File? — Default: None
???

augur_from_mltree.ancestral_traits_to_infer
Array[String]? — Default: None
A list of metadata traits to use for ancestral node inference (see https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/traits.html). Multiple traits may be specified; must correspond exactly to column headers in metadata file. Omitting these values will skip ancestral trait inference, and ancestral nodes will not have estimated values for metadata.

augur_from_mltree.ancestral_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

augur_from_mltree.ancestral_tree.inference
String — Default: "joint"
???

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

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

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

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

augur_from_mltree.assign_clades_to_nodes.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_mltree.clades_tsv
File? — Default: None
A TSV file containing clade mutation positions in four columns: [clade gene site alt]; see: https://nextstrain.org/docs/tutorials/defining-clades

augur_from_mltree.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???

augur_from_mltree.export_auspice_json.colors_tsv
File? — Default: None
???

augur_from_mltree.export_auspice_json.description_md
File? — Default: None
???

augur_from_mltree.export_auspice_json.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_mltree.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???

augur_from_mltree.export_auspice_json.lat_longs_tsv
File? — Default: None
???

augur_from_mltree.export_auspice_json.maintainers
Array[String]? — Default: None
???

augur_from_mltree.export_auspice_json.title
String? — Default: None
???

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

augur_from_mltree.refine_augur_tree.clock_filter_iqd
Int? — Default: 4
???

augur_from_mltree.refine_augur_tree.clock_rate
Float? — Default: None
???

augur_from_mltree.refine_augur_tree.clock_std_dev
Float? — Default: None
???

augur_from_mltree.refine_augur_tree.coalescent
String? — Default: None
???

augur_from_mltree.refine_augur_tree.covariance
Boolean? — Default: None
???

augur_from_mltree.refine_augur_tree.date_confidence
Boolean — Default: true
???

augur_from_mltree.refine_augur_tree.date_inference
String? — Default: "marginal"
???

augur_from_mltree.refine_augur_tree.divergence_units
String? — Default: "mutations"
???

augur_from_mltree.refine_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

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

augur_from_mltree.refine_augur_tree.keep_root
Boolean — Default: true
???

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

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

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

augur_from_mltree.translate_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

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

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

augur_from_msa¶

Build trees, and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/

Inputs¶

Required inputs¶

augur_from_msa.auspice_config
File — Default: None
A file specifying options to customize the auspice export; see: https://nextstrain.github.io/auspice/customise-client/introduction

augur_from_msa.genbank_gb
File — Default: None
A 'genbank' formatted gene annotation file that is used to calculate coding consequences of observed mutations. Must correspond to the same coordinate space as ref_fasta. Typically downloaded from the same NCBI accession number as ref_fasta.

augur_from_msa.msa_or_vcf
File — Default: None
Multiple sequence alignment (aligned fasta) or variants (vcf format).

augur_from_msa.ref_fasta
File — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar.

augur_from_msa.sample_metadata
Array[File]+ — Default: None
Metadata in tab-separated text format. See https://nextstrain-augur.readthedocs.io/en/stable/faq/metadata.html for details. At least one tab file must be provided--if multiple are provided, they will be joined via a full left outer join using the 'strain' column as the join ID.

Other inputs¶

Show/Hide

augur_from_msa.ancestral_traits.confidence
Boolean — Default: true
???

augur_from_msa.ancestral_traits.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_msa.ancestral_traits.sampling_bias_correction
Float? — Default: None
???

augur_from_msa.ancestral_traits.weights
File? — Default: None
???

augur_from_msa.ancestral_traits_to_infer
Array[String]? — Default: None
A list of metadata traits to use for ancestral node inference (see https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/traits.html). Multiple traits may be specified; must correspond exactly to column headers in metadata file. Omitting these values will skip ancestral trait inference, and ancestral nodes will not have estimated values for metadata.

augur_from_msa.ancestral_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

augur_from_msa.ancestral_tree.inference
String — Default: "joint"
???

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

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

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

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

augur_from_msa.assign_clades_to_nodes.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_msa.augur_mask_sites.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_msa.clades_tsv
File? — Default: None
A TSV file containing clade mutation positions in four columns: [clade gene site alt]; see: https://nextstrain.org/docs/tutorials/defining-clades

augur_from_msa.draft_augur_tree.cpus
Int? — Default: None
???

augur_from_msa.draft_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

augur_from_msa.draft_augur_tree.method
String — Default: "iqtree"
???

augur_from_msa.draft_augur_tree.substitution_model
String — Default: "GTR"
???

augur_from_msa.draft_augur_tree.tree_builder_args
String? — Default: None
???

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

augur_from_msa.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???

augur_from_msa.export_auspice_json.colors_tsv
File? — Default: None
???

augur_from_msa.export_auspice_json.description_md
File? — Default: None
???

augur_from_msa.export_auspice_json.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_msa.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???

augur_from_msa.export_auspice_json.lat_longs_tsv
File? — Default: None
???

augur_from_msa.export_auspice_json.maintainers
Array[String]? — Default: None
???

augur_from_msa.export_auspice_json.title
String? — Default: None
???

augur_from_msa.filter_sequences_to_list.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

augur_from_msa.keep_list
Array[File]? — Default: None
Optional lists of strain ids to filter inputs down to.

augur_from_msa.mask_bed
File? — Default: None
Optional list of sites to mask when building trees.

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

augur_from_msa.refine_augur_tree.clock_filter_iqd
Int? — Default: 4
???

augur_from_msa.refine_augur_tree.clock_rate
Float? — Default: None
???

augur_from_msa.refine_augur_tree.clock_std_dev
Float? — Default: None
???

augur_from_msa.refine_augur_tree.coalescent
String? — Default: None
???

augur_from_msa.refine_augur_tree.covariance
Boolean? — Default: None
???

augur_from_msa.refine_augur_tree.date_confidence
Boolean — Default: true
???

augur_from_msa.refine_augur_tree.date_inference
String? — Default: "marginal"
???

augur_from_msa.refine_augur_tree.divergence_units
String? — Default: "mutations"
???

augur_from_msa.refine_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

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

augur_from_msa.refine_augur_tree.keep_root
Boolean — Default: true
???

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

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

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

augur_from_msa.translate_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

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

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

augur_from_msa.tsv_join.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

bams_multiqc¶

Run FastQC on a set of BAM files, and then MultiQC to summarize all outputs.

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:2.1.19"
???

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
???

beast_gpu¶

Runs BEAST (v1) on a GPU instance. Use with care–this can be expensive if run incorrectly.

Inputs¶

Required inputs¶

beast_gpu.beast.beauti_xml
File — Default: None
???

Other inputs¶

Show/Hide

beast_gpu.beast.accelerator_count
Int? — Default: None
???

beast_gpu.beast.accelerator_type
String? — Default: None
???

beast_gpu.beast.docker
String — Default: "quay.io/broadinstitute/beast-beagle-cuda:1.10.5pre"
???

beast_gpu.beast.gpu_count
Int? — Default: None
???

beast_gpu.beast.gpu_type
String? — Default: None
???

classify_kaiju¶

Taxonomic classification of reads with 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:2.1.16.0"
???

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

classify_kraken2¶

Taxonomic classification of sequences via kraken2 (or kraken2x, depending on the database provided).

Inputs¶

Required inputs¶

classify_kraken2.kraken2.kraken2_db_tgz
File — Default: None
Pre-built Kraken database tarball containing three files: hash.k2d, opts.k2d, and taxo.k2d.

classify_kraken2.kraken2.krona_taxonomy_db_tgz
File — Default: None
Krona taxonomy database containing a single file: taxonomy.tab, or possibly just a compressed taxonomy.tab

classify_kraken2.kraken2.reads_bam
File — Default: None
Reads or contigs to classify. May be unmapped or mapped or both, paired-end or single-end.

Other inputs¶

Show/Hide

classify_kraken2.kraken2.confidence_threshold
Float? — Default: None
Kraken2 confidence score threshold (0.0-1.0). See https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#confidence-scoring

classify_kraken2.kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

classify_kraken2.kraken2.machine_mem_gb
Int? — Default: None
???

classify_kraken2.kraken2.min_base_qual
Int? — Default: None
Minimum base quality used in classification

classify_krakenuniq¶

Taxonomic classification of reads using krakenuniq v1.

Inputs¶

Required inputs¶

classify_krakenuniq.krakenuniq.krakenuniq_db_tar_lz4
File — Default: None
Pre-built Kraken database tarball.

classify_krakenuniq.krakenuniq.krona_taxonomy_db_tgz
File — Default: None
Krona taxonomy database containing a single file: taxonomy.tab, or possibly just a compressed taxonomy.tab

classify_krakenuniq.krakenuniq.reads_unmapped_bam
Array[File] — Default: None
Reads to classify. May be unmapped or mapped or both, paired-end or single-end.

Other inputs¶

Show/Hide

classify_krakenuniq.krakenuniq.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

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:2.1.16.0"
???

classify_multi¶

Runs raw reads through taxonomic classification (Kraken2), human read depletion (based on Kraken2), de novo assembly (SPAdes), and FASTQC/multiQC of reads.

Inputs¶

Required inputs¶

classify_multi.kraken2_db_tgz
File — Default: None
Pre-built Kraken database tarball containing three files: hash.k2d, opts.k2d, and taxo.k2d.

classify_multi.krona_taxonomy_db_kraken2_tgz
File — Default: None
Krona taxonomy database containing a single file: taxonomy.tab, or possibly just a compressed taxonomy.tab

classify_multi.ncbi_taxdump_tgz
File — Default: None
An NCBI taxdump.tar.gz file that contains, at the minimum, a nodes.dmp and names.dmp file.

classify_multi.reads_bams
Array[File]+ — Default: None
Reads to classify. May be unmapped or mapped or both, paired-end or single-end.

classify_multi.spikein_db
File — Default: None
ERCC spike-in sequences

classify_multi.trim_clip_db
File — Default: None
Adapter sequences to remove via trimmomatic prior to SPAdes assembly

Other inputs¶

Show/Hide

classify_multi.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

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

classify_multi.deplete.minimum_hit_groups
Int? — Default: None
???

classify_multi.deplete.taxonomic_ids
Array[Int]? — Default: None
???

classify_multi.deplete.withoutChildren
Boolean — Default: false
???

classify_multi.fastqc_cleaned.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

classify_multi.fastqc_raw.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

classify_multi.filter_acellular.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

classify_multi.filter_acellular.machine_mem_gb
Int? — Default: None
???

classify_multi.filter_acellular.minimum_hit_groups
Int? — Default: None
???

classify_multi.filter_acellular.taxonomic_ids
Array[Int]? — Default: None
???

classify_multi.filter_acellular.withoutChildren
Boolean — Default: false
???

classify_multi.kraken2.confidence_threshold
Float? — Default: None
Kraken2 confidence score threshold (0.0-1.0). See https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#confidence-scoring

classify_multi.kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

classify_multi.kraken2.machine_mem_gb
Int? — Default: None
???

classify_multi.kraken2.min_base_qual
Int? — Default: None
Minimum base quality used in classification

classify_multi.krona_merge_kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

classify_multi.krona_merge_kraken2.machine_mem_gb
Int? — Default: None
???

classify_multi.krona_merge_kraken2.magnitude_column
Int? — Default: None
???

classify_multi.krona_merge_kraken2.query_column
Int? — Default: None
???

classify_multi.krona_merge_kraken2.score_column
Int? — Default: None
???

classify_multi.krona_merge_kraken2.taxid_column
Int? — Default: None
???

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

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

classify_multi.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_multi.metag_summary_report.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

classify_multi.rmdup_ubam.docker
String? — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

classify_multi.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

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

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

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

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

classify_multi.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

classify_multi.spike_summary.output_prefix
String — Default: "count_summary"
???

classify_multi.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

classify_single¶

Runs raw reads through taxonomic classification (Kraken2), human read depletion (based on Kraken2), de novo assembly (SPAdes), and FASTQC/multiQC of reads.

Inputs¶

Required inputs¶

classify_single.kraken2_db_tgz
File — Default: None
Pre-built Kraken database tarball containing three files: hash.k2d, opts.k2d, and taxo.k2d.

classify_single.krona_taxonomy_db_kraken2_tgz
File — Default: None
Krona taxonomy database containing a single file: taxonomy.tab, or possibly just a compressed taxonomy.tab

classify_single.ncbi_taxdump_tgz
File — Default: None
An NCBI taxdump.tar.gz file that contains, at the minimum, a nodes.dmp and names.dmp file.

classify_single.reads_bam
File — Default: None
Reads to classify. May be unmapped or mapped or both, paired-end or single-end.

classify_single.spikein_db
File — Default: None
ERCC spike-in sequences

classify_single.trim_clip_db
File — Default: None
Adapter sequences to remove via trimmomatic prior to SPAdes assembly

Other inputs¶

Show/Hide

classify_single.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

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

classify_single.deplete.minimum_hit_groups
Int? — Default: None
???

classify_single.deplete.taxonomic_ids
Array[Int]? — Default: None
???

classify_single.deplete.withoutChildren
Boolean — Default: false
???

classify_single.fastqc_cleaned.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

classify_single.fastqc_raw.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

classify_single.filter_acellular.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

classify_single.filter_acellular.machine_mem_gb
Int? — Default: None
???

classify_single.filter_acellular.minimum_hit_groups
Int? — Default: None
???

classify_single.filter_acellular.taxonomic_ids
Array[Int]? — Default: None
???

classify_single.filter_acellular.withoutChildren
Boolean — Default: false
???

classify_single.kraken2.confidence_threshold
Float? — Default: None
Kraken2 confidence score threshold (0.0-1.0). See https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#confidence-scoring

classify_single.kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

classify_single.kraken2.machine_mem_gb
Int? — Default: None
???

classify_single.kraken2.min_base_qual
Int? — Default: None
Minimum base quality used in classification

classify_single.rmdup_ubam.docker
String? — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

classify_single.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

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

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

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

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

classify_single.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

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:2.1.16.0"
???

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:2.1.19"
???

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:2.1.16.1"
???

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
???

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:2.1.19"
???

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

demux_deplete¶

Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory, followed by QC metrics, depletion, and SRA submission prep.

Inputs¶

Required inputs¶

demux_deplete.flowcell_tgz
File — Default: None
Illumina BCL directory compressed as tarball. Must contain RunInfo.xml, SampleSheet.csv, RTAComplete.txt, and Data/Intensities/BaseCalls/*

demux_deplete.samplesheets
Array[File]+ — Default: None
Custom formatted 'extended' format tsv samplesheets that will override any SampleSheet.csv in the illumina BCL directory. Must supply one file per lane of the flowcell, and must provide them in lane order. Required tsv column headings are: sample, library_id_per_sample, barcode_1, barcode_2 (if paired reads, omit if single-end), library_strategy, library_source, library_selection, design_description. 'sample' must correspond to a biological sample. 'sample' x 'library_id_per_sample' must be unique within a samplesheet and correspond to independent libraries from the same original sample. barcode_1 and barcode_2 must correspond to the actual index sequence. Remaining columns must follow strict ontology: see 3rd tab of https://www.ncbi.nlm.nih.gov/core/assets/sra/files/SRA_metadata_acc_example.xlsx for controlled vocabulary and term definitions.

demux_deplete.spikein_db
File — Default: None
???

Other inputs¶

Show/Hide

demux_deplete.biosample_map
File? — Default: None
A two-column tsv that contains at least the following columns: sample_name, accession. sample_name refers to the external sample id, accession is the NCBI BioSample accession number (SAMNxxx). If this file is omitted, SRA submission prep will be skipped.

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

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

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

demux_deplete.default_filename_keys
Array[String] — Default: ["spike_in"]
???

demux_deplete.default_sample_keys
Array[String] — Default: ["amplicon_set", "control"]
???

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

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

demux_deplete.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

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

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

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

demux_deplete.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

demux_deplete.instrument_model
String? — Default: None
???

demux_deplete.min_reads_per_bam
Int — Default: 100
???

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

demux_deplete.sample_rename_map
File? — Default: None
If 'samples' need to be renamed, provide a two-column tsv that contains at least the following columns: internal_id, external_id. All samples will be renamed prior to analysis. Any samples described in the samplesheets that are not present in sample_rename_map will be unaltered. If this is omitted, no samples will be renamed.

demux_deplete.samplesheet_rename_ids.new_id_col
String — Default: 'external_id'
???

demux_deplete.samplesheet_rename_ids.old_id_col
String — Default: 'internal_id'
???

demux_deplete.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

demux_deplete.spike_summary.output_prefix
String — Default: "count_summary"
???

demux_deplete.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

demux_deplete.sra_meta_prep.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

demux_deplete.sra_title
String? — Default: None
???

demux_metag¶

Inputs¶

Required inputs¶

demux_metag.blast_db_tgz
File — Default: None
???

demux_metag.illumina_demux.flowcell_tgz
File — Default: None
Illumina BCL directory compressed as tarball. Must contain RunInfo.xml (unless overridden by runinfo), SampleSheet.csv (unless overridden by samplesheet), RTAComplete.txt, and Data/Intensities/BaseCalls/*

demux_metag.kraken2_db_tgz
File — Default: None
???

demux_metag.krona_taxonomy_db_blast_tgz
File — Default: None
???

demux_metag.krona_taxonomy_db_kraken2_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.blastx.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

demux_metag.blastx.machine_mem_gb
Int? — 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:2.1.16.0"
???

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:2.1.19"
???

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.kraken2.confidence_threshold
Float? — Default: None
Kraken2 confidence score threshold (0.0-1.0). See https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#confidence-scoring

demux_metag.kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

demux_metag.kraken2.machine_mem_gb
Int? — Default: None
???

demux_metag.kraken2.min_base_qual
Int? — Default: None
Minimum base quality used in classification

demux_metag.krona_merge_blastx.docker
String — Default: "biocontainers/krona:v2.7.1_cv1"
???

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

demux_metag.krona_merge_kraken2.docker
String — Default: "biocontainers/krona:v2.7.1_cv1"
???

demux_metag.krona_merge_kraken2.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:2.1.16.0"
???

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:2.1.19"
???

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:2.1.16.1"
???

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.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

demux_metag.spike_summary.output_prefix
String — Default: "count_summary"
???

demux_metag.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

demux_only¶

Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory.

Inputs¶

Required inputs¶

demux_only.illumina_demux.flowcell_tgz
File — Default: None
Illumina BCL directory compressed as tarball. Must contain RunInfo.xml (unless overridden by runinfo), SampleSheet.csv (unless overridden by samplesheet), RTAComplete.txt, and Data/Intensities/BaseCalls/*

Other inputs¶

Show/Hide

demux_only.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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¶

Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory, followed by basic metagenomics and QC metrics. Intended for automatic triggering post upload on DNAnexus.

Inputs¶

Required inputs¶

demux_plus.illumina_demux.flowcell_tgz
File — Default: None
Illumina BCL directory compressed as tarball. Must contain RunInfo.xml (unless overridden by runinfo), SampleSheet.csv (unless overridden by samplesheet), RTAComplete.txt, and Data/Intensities/BaseCalls/*

demux_plus.krakenuniq.krakenuniq_db_tar_lz4
File — Default: None
Pre-built Kraken database tarball.

demux_plus.krakenuniq.krona_taxonomy_db_tgz
File — Default: None
Krona taxonomy database containing a single file: taxonomy.tab, or possibly just a compressed taxonomy.tab

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:2.1.16.0"
???

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:2.1.19"
???

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:2.1.16.0"
???

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:2.1.16.0"
???

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:2.1.16.1"
???

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.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

demux_plus.spike_summary.output_prefix
String — Default: "count_summary"
???

demux_plus.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

deplete_only¶

Taxonomic depletion of reads matching unwanted taxa (such as human).

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:2.1.16.0"
???

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"
???

diff_genome_sets¶

Inputs¶

Required inputs¶

diff_genome_sets.genome_set_one
Array[File] — Default: None
???

diff_genome_sets.genome_set_two
Array[File] — Default: None
???

Other inputs¶

Show/Hide

diff_genome_sets.compare_two_genomes.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

diff_genome_sets.tsv_stack.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

downsample¶

Random subsampling of reads.

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:2.1.19"
???

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

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

fastq_to_ubam¶

Convert reads from fastq format (single or paired) to unaligned BAM format.

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:2.1.19"
???

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:2.1.16.0"
???

fetch_sra_to_bam¶

Retrieve reads from the NCBI Short Read Archive in unaligned BAM format with relevant metadata encoded.

Inputs¶

Required inputs¶

fetch_sra_to_bam.Fetch_SRA_to_BAM.SRA_ID
String — Default: None
???

Other inputs¶

Show/Hide

fetch_sra_to_bam.Fetch_SRA_to_BAM.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.1"
???

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

filter_classified_bam_to_taxa¶

Taxonomic filtration of reads utilizing output from a classifier such as kraken1/2/uniq. Can filter out or filter to a specified taxonomic grouping.

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:2.1.16.0"
???

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

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

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

filter_classified_bam_to_taxa.filter_bam_to_taxa.out_filename_suffix
String — Default: "filtered"
???

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
???

filter_sequences¶

Filter and subsample a sequence set. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/filter.html

Inputs¶

Required inputs¶

filter_sequences.filter.sample_metadata_tsv
File — Default: None
Metadata in tab-separated text format. See https://nextstrain-augur.readthedocs.io/en/stable/faq/metadata.html for details.

filter_sequences.filter.sequences_fasta
File — Default: None
Set of sequences (unaligned fasta or aligned fasta -- one sequence per genome) or variants (vcf format) to subsample using augur filter.

Other inputs¶

Show/Hide

filter_sequences.filter.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

filter_sequences.filter.exclude
File? — Default: None
???

filter_sequences.filter.exclude_where
Array[String]? — Default: None
???

filter_sequences.filter.group_by
String? — Default: None
???

filter_sequences.filter.include
File? — Default: None
???

filter_sequences.filter.include_where
Array[String]? — Default: None
???

filter_sequences.filter.max_date
Float? — Default: None
???

filter_sequences.filter.min_date
Float? — Default: None
???

filter_sequences.filter.min_length
Int? — Default: None
???

filter_sequences.filter.non_nucleotide
Boolean — Default: true
???

filter_sequences.filter.priority
File? — Default: None
???

filter_sequences.filter.sequences_per_group
Int? — Default: None
???

filter_sequences.filter.subsample_seed
Int? — Default: None
???

genbank¶

Prepare assemblies for Genbank submission. This includes annotation by simple coordinate transfer from Genbank annotations and a multiple alignment. See https://viral-pipelines.readthedocs.io/en/latest/ncbi_submission.html for details.

Inputs¶

Required inputs¶

genbank.assemblies_fasta
Array[File]+ — Default: None
Genomes to prepare for Genbank submission. One file per genome: all segments/chromosomes included in one file. All fasta files must contain exactly the same number of sequences as reference_fasta (which must equal the number of files in reference_annot_tbl).

genbank.authors_sbt
File — Default: None
A genbank submission template file (SBT) with the author list, created at https://submit.ncbi.nlm.nih.gov/genbank/template/submission/

genbank.biosample_attributes
File — Default: None
A post-submission attributes file from NCBI BioSample, which is available at https://submit.ncbi.nlm.nih.gov/subs/ and clicking on 'Download attributes file with BioSample accessions'.

genbank.reference_fastas
Array[File]+ — Default: None
Reference genome, each segment/chromosome in a separate fasta file, in the exact same count and order as the segments/chromosomes described in genome_fasta. Headers must be Genbank accessions.

genbank.reference_feature_tables
Array[File]+ — Default: None
NCBI Genbank feature table, each segment/chromosome in a separate TBL file, in the exact same count and order as the segments/chromosomes described in genome_fasta and reference_fastas. Accession numbers in the TBL files must correspond exactly to those in reference_fasta.

genbank.taxid
Int — Default: None
The NCBI taxonomy ID for the species being submitted in this batch (all sequences in this batch must belong to the same taxid). https://www.ncbi.nlm.nih.gov/taxonomy/

Other common inputs¶

genbank.coverage_table
File? — Default: None
A two column tab text file mapping sample IDs (first column) to average sequencing coverage (second column, floating point number).

genbank.molType
String? — Default: 'cRNA'
The type of molecule being described. This defaults to 'cRNA' as this pipeline is most commonly used for viral submissions, but any value allowed by the INSDC controlled vocabulary may be used here. Valid values are described at http://www.insdc.org/controlled-vocabulary-moltype-qualifier

genbank.organism
String? — Default: None
The scientific name for the organism being submitted. This is typically the species name and should match the name given by the NCBI Taxonomy database. For more info, see: https://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html#Organism

genbank.sequencingTech
String? — Default: None
The type of sequencer used to generate reads. NCBI has a controlled vocabulary for this value which can be found here: https://submit.ncbi.nlm.nih.gov/structcomment/nongenomes/

Other inputs¶

Show/Hide

genbank.annot.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

genbank.biosample_to_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

genbank.biosample_to_genbank.filter_to_ids
File? — Default: None
???

genbank.comment
String? — Default: None
Optional comments that can be displayed in the COMMENT section of the Genbank record. This may include any disclaimers about assembly quality or notes about pre-publication availability or requests to discuss pre-publication use with authors.

genbank.prep_genbank.assembly_method
String? — Default: None
Very short description of the software approach used to assemble the genome. We typically provide a github link here. If this is specified, assembly_method_version should also be specified.

genbank.prep_genbank.assembly_method_version
String? — Default: None
The version of the software used. If this is specified, assembly_method should also be specified.

genbank.prep_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

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

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:2.1.16.0"
???

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:2.1.16.0"
???

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¶

Intrahost variant calling with V-Phaser2. Requires an assembled genome and a BAM of aligned reads against that same genome.

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:2.1.16.0"
???

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.removeDoublyMappedReads
Boolean — Default: true
???

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
???

kraken2_build¶

Build a Kraken2 (or 2X) database.

Inputs¶

Required inputs¶

kraken2_build.build_kraken2_db.db_basename
String — Default: None
A descriptive string used in output filenames. Outputs will be called kraken2-.tar.zst, krona-.tar.zst, and taxdump-.tar.gz

Other inputs¶

Show/Hide

kraken2_build.build_kraken2_db.custom_libraries
Array[File] — Default: []
A list of 'custom' kraken2 databases to include in this build. Headers must be formatted as described in the kraken2 documentation. These are fastas or tarball collections of such fastas--multiple may be provided here.

kraken2_build.build_kraken2_db.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

kraken2_build.build_kraken2_db.kmerLen
Int? — Default: None
(k) K-mer length in bp/aa (Kraken2 defaults: 35 nt, 15 aa)

kraken2_build.build_kraken2_db.machine_mem_gb
Int? — Default: None
???

kraken2_build.build_kraken2_db.maxDbSize
Int? — Default: None
???

kraken2_build.build_kraken2_db.minimizerLen
Int? — Default: None
(l) Minimizer length in bp/aa (Kraken2 defaults: 31 nt, 12 aa)

kraken2_build.build_kraken2_db.minimizerSpaces
Int? — Default: None
(s) Number of bp/aa in minimizer that are ignored in comparisons (Kraken2 defaults: 7 nt, 0 aa)

kraken2_build.build_kraken2_db.protein
Boolean — Default: false
Build a protein (translated search) database. Default is nucleotide.

kraken2_build.build_kraken2_db.standard_libraries
Array[String] — Default: ["archaea", "bacteria", "plasmid", "viral", "human", "fungi", "protozoa", "UniVec_Core"]
A list of 'standard' kraken2 databases to include in this build. Including any values here will cause fresh downloads of data at the time of build. A list of acceptable names is available at https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#custom-databases

kraken2_build.build_kraken2_db.taxonomy_db_tgz
File? — Default: None
Optional tarball of kraken2 taxonomy database directory. Omitting this input will cause a fresh download from NCBI at the time of build.

kraken2_build.build_kraken2_db.zstd_compression_level
Int? — Default: None
???

mafft¶

MAFFT multiple-alignment for a set of possibly multi-segment genomes.

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:2.1.16.0"
???

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_snp¶

Align assemblies with mafft and find SNPs with snp-sites.

Inputs¶

Required inputs¶

mafft_and_snp.assembly_fastas
Array[File] — Default: None
Set of assembled genomes to align and build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.

mafft_and_snp.min_unambig_genome
Int — Default: None
Minimum number of called bases in genome to pass prefilter.

mafft_and_snp.ref_fasta
File — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar. Uncompressed.

Other inputs¶

Show/Hide

mafft_and_snp.draft_augur_tree.cpus
Int? — Default: None
???

mafft_and_snp.draft_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

mafft_and_snp.draft_augur_tree.method
String — Default: "iqtree"
???

mafft_and_snp.draft_augur_tree.substitution_model
String — Default: "GTR"
???

mafft_and_snp.draft_augur_tree.tree_builder_args
String? — Default: None
???

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

mafft_and_snp.filter_sequences_by_length.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

mafft_and_snp.gzcat.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

mafft_and_snp.mafft.cpus
Int — Default: 32
???

mafft_and_snp.mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

mafft_and_snp.mafft.keep_length
Boolean — Default: true
???

mafft_and_snp.mafft.large
Boolean — Default: false
???

mafft_and_snp.mafft.mem_size
Int — Default: 250
???

mafft_and_snp.mafft.memsavetree
Boolean — Default: false
???

mafft_and_snp.mafft.remove_reference
Boolean — Default: false
???

mafft_and_snp.run_iqtree
Boolean — Default: false
???

mafft_and_snp.snp_sites.allow_wildcard_bases
Boolean — Default: true
???

mafft_and_snp.snp_sites.docker
String — Default: "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
???

mafft_and_snp_annotated¶

Align assemblies with mafft and find SNPs with snp-sites.

Inputs¶

Required inputs¶

mafft_and_snp_annotated.assembly_fastas
Array[File] — Default: None
Set of assembled genomes to align and build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.

mafft_and_snp_annotated.min_unambig_genome
Int — Default: None
Minimum number of called bases in genome to pass prefilter.

mafft_and_snp_annotated.ref_fasta
File — Default: None
A reference assembly (not included in assembly_fastas) to align assembly_fastas against. Typically from NCBI RefSeq or similar. Uncompressed.

Other inputs¶

Show/Hide

mafft_and_snp_annotated.annotate_vcf.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

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

mafft_and_snp_annotated.annotate_vcf.machine_mem_gb
Int? — Default: None
???

mafft_and_snp_annotated.annotate_vcf.output_basename
String — Default: basename(basename(in_vcf,".gz"),".vcf")
???

mafft_and_snp_annotated.annotate_vcf.snpEffRef
Array[String]? — Default: None
list of accessions to build/find snpEff database. If this is not provided, the ID from the reference fasta will be used (it must be a GenBank accession)

mafft_and_snp_annotated.draft_augur_tree.cpus
Int? — Default: None
???

mafft_and_snp_annotated.draft_augur_tree.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

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

mafft_and_snp_annotated.draft_augur_tree.method
String — Default: "iqtree"
???

mafft_and_snp_annotated.draft_augur_tree.substitution_model
String — Default: "GTR"
???

mafft_and_snp_annotated.draft_augur_tree.tree_builder_args
String? — Default: None
???

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

mafft_and_snp_annotated.filter_sequences_by_length.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

mafft_and_snp_annotated.gzcat.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

mafft_and_snp_annotated.mafft.cpus
Int — Default: 32
???

mafft_and_snp_annotated.mafft.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

mafft_and_snp_annotated.mafft.keep_length
Boolean — Default: true
???

mafft_and_snp_annotated.mafft.large
Boolean — Default: false
???

mafft_and_snp_annotated.mafft.mem_size
Int — Default: 250
???

mafft_and_snp_annotated.mafft.memsavetree
Boolean — Default: false
???

mafft_and_snp_annotated.mafft.remove_reference
Boolean — Default: false
???

mafft_and_snp_annotated.run_iqtree
Boolean — Default: false
???

mafft_and_snp_annotated.snp_sites.allow_wildcard_bases
Boolean — Default: true
???

mafft_and_snp_annotated.snp_sites.docker
String — Default: "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
???

mafft_and_trim¶

MAFFT based multiple alignment followed by trimal-based edge trimming.

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:2.1.16.0"
???

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¶

Merge, reheader, or merge-and-reheader BAM files.

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:2.1.19"
???

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

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

merge_metagenomics¶

Combine metagenomic reports from single samples into an aggregate report.

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:2.1.16.0"
???

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¶

Combine multiple tar files (possibly compressed by gzip, bz2, lz4, zstd, etc) into a single tar file. Originally meant for combining streaming upload chunks from a sequencing run.

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:2.1.19"
???

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

merge_vcfs¶

Merge VCFs from multiple samples using GATK3.

Inputs¶

Required inputs¶

merge_vcfs.merge_vcfs_gatk.in_vcfs_gz
Array[File] — Default: None
VCF files to merged; should be (b)gzipped.

merge_vcfs.merge_vcfs_gatk.ref_fasta
File — Default: None
fasta file of reference genome relative to which the input VCF sites were called

Other inputs¶

Show/Hide

merge_vcfs.merge_vcfs_gatk.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

merge_vcfs.merge_vcfs_gatk.machine_mem_gb
Int? — Default: None
???

merge_vcfs.merge_vcfs_gatk.output_prefix
String — Default: "merged"
???

merge_vcfs_and_annotate¶

Merge VCFs emitted by GATK UnifiedGenotyper and annotate with snpEff.

Inputs¶

Required inputs¶

merge_vcfs_and_annotate.merge_vcfs.in_vcfs_gz
Array[File] — Default: None
VCF files to merged; should be (b)gzipped.

merge_vcfs_and_annotate.reference_fasta
File — Default: None
Reference genome, all segments/chromosomes in one fasta file. Headers must be Genbank accessions.

Other inputs¶

Show/Hide

merge_vcfs_and_annotate.annotate_vcf.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

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

merge_vcfs_and_annotate.annotate_vcf.machine_mem_gb
Int? — Default: None
???

merge_vcfs_and_annotate.annotate_vcf.output_basename
String — Default: basename(basename(in_vcf,".gz"),".vcf")
???

merge_vcfs_and_annotate.annotate_vcf.snpEffRef
Array[String]? — Default: None
list of accessions to build/find snpEff database. If this is not provided, the ID from the reference fasta will be used (it must be a GenBank accession)

merge_vcfs_and_annotate.merge_vcfs.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

merge_vcfs_and_annotate.merge_vcfs.machine_mem_gb
Int? — Default: None
???

merge_vcfs_and_annotate.merge_vcfs.output_prefix
String — Default: "merged"
???

multiqc_only¶

Combine multiple FastQC reports into a single MultiQC summary.

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
???

sarscov2_genbank¶

Prepare SARS-CoV-2 assemblies for Genbank submission. This includes QC checks with NCBI’s VADR tool and filters out genomes that do not pass its tests.

Inputs¶

Required inputs¶

sarscov2_genbank.assemblies_fasta
Array[File]+ — Default: None
Genomes to prepare for Genbank submission. One file per genome: all segments/chromosomes included in one file. All fasta files must contain exactly the same number of sequences as reference_fasta (which must equal the number of files in reference_annot_tbl).

sarscov2_genbank.assembly_stats_tsv
File — Default: None
A four column tab text file with one row per sequence and the following header columns: SeqID, Assembly Method, Coverage, Sequencing Technology

sarscov2_genbank.authors_sbt
File — Default: None
A genbank submission template file (SBT) with the author list, created at https://submit.ncbi.nlm.nih.gov/genbank/template/submission/

sarscov2_genbank.biosample_attributes
File — Default: None
A post-submission attributes file from NCBI BioSample, which is available at https://submit.ncbi.nlm.nih.gov/subs/ and clicking on 'Download attributes file with BioSample accessions'.

sarscov2_genbank.package_genbank_ftp_submission.account_name
String — Default: None
???

sarscov2_genbank.package_genbank_ftp_submission.spuid_namespace
String — Default: None
???

sarscov2_genbank.package_genbank_ftp_submission.submission_name
String — Default: None
???

sarscov2_genbank.package_genbank_ftp_submission.submission_uid
String — Default: None
???

Other inputs¶

Show/Hide

sarscov2_genbank.assembly_bases.docker
String — Default: "ubuntu"
???

sarscov2_genbank.biosample_to_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

sarscov2_genbank.fasta_rename_map
File? — Default: None
???

sarscov2_genbank.gisaid_meta_prep.authors
String? — Default: None
???

sarscov2_genbank.gisaid_meta_prep.continent
String — Default: "North America"
???

sarscov2_genbank.gisaid_meta_prep.fasta_filename
String? — Default: None
???

sarscov2_genbank.gisaid_meta_prep.originating_lab_addr
String? — Default: None
???

sarscov2_genbank.gisaid_meta_prep.strict
Boolean — Default: true
???

sarscov2_genbank.gisaid_meta_prep.submitting_lab_addr
String? — Default: None
???

sarscov2_genbank.gisaid_meta_prep.submitting_lab_name
String? — Default: None
???

sarscov2_genbank.gisaid_meta_prep.username
String? — Default: None
???

sarscov2_genbank.gisaid_prefix
String — Default: 'hCoV-19/'
???

sarscov2_genbank.min_genome_bases
Int — Default: 20000
???

sarscov2_genbank.package_genbank_ftp_submission.docker
String — Default: "quay.io/broadinstitute/viral-baseimage:0.1.20"
???

sarscov2_genbank.prefix_gisaid.out_basename
String — Default: basename(genome_fasta,".fasta")
???

sarscov2_genbank.rename_fasta_header.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_genbank.rename_fasta_header.out_basename
String — Default: basename(genome_fasta,".fasta")
???

sarscov2_genbank.structured_comments.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_genbank.taxid
Int — Default: 2697049
???

sarscov2_genbank.vadr.docker
String — Default: "staphb/vadr:1.1.2"
???

sarscov2_genbank.vadr.vadr_opts
String — Default: "-s -r --nomisc --mkey NC_045512 --lowsim5term 2 --lowsim3term 2 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf"
???

sarscov2_illumina_full¶

Full SARS-CoV-2 analysis workflow starting from raw Illumina flowcell (tar.gz) and metadata and performing assembly, spike-in analysis, qc, lineage assignment, and packaging for data release.

Inputs¶

Required inputs¶

sarscov2_illumina_full.amplicon_bed_prefix
String — Default: None
amplicon primers to trim in reference coordinate space (0-based BED format)

sarscov2_illumina_full.biosample_attributes
Array[File] — Default: None
A post-submission attributes file from NCBI BioSample, which is available at https://submit.ncbi.nlm.nih.gov/subs/ and clicking on 'Download attributes file with BioSample accessions'. The 'sample_name' column must match the external_ids used in sample_rename_map (or internal ids if sample_rename_map is omitted).

sarscov2_illumina_full.demux_deplete.samplesheets
Array[File]+ — Default: None
Custom formatted 'extended' format tsv samplesheets that will override any SampleSheet.csv in the illumina BCL directory. Must supply one file per lane of the flowcell, and must provide them in lane order. Required tsv column headings are: sample, library_id_per_sample, barcode_1, barcode_2 (if paired reads, omit if single-end), library_strategy, library_source, library_selection, design_description. 'sample' must correspond to a biological sample. 'sample' x 'library_id_per_sample' must be unique within a samplesheet and correspond to independent libraries from the same original sample. barcode_1 and barcode_2 must correspond to the actual index sequence. Remaining columns must follow strict ontology: see 3rd tab of https://www.ncbi.nlm.nih.gov/core/assets/sra/files/SRA_metadata_acc_example.xlsx for controlled vocabulary and term definitions.

sarscov2_illumina_full.demux_deplete.spikein_db
File — Default: None
???

sarscov2_illumina_full.flowcell_tgz
File — Default: None
???

sarscov2_illumina_full.instrument_model
String — Default: None
???

sarscov2_illumina_full.package_genbank_ftp_submission.account_name
String — Default: None
???

sarscov2_illumina_full.package_genbank_ftp_submission.author_template_sbt
File — Default: None
???

sarscov2_illumina_full.package_genbank_ftp_submission.spuid_namespace
String — Default: None
???

sarscov2_illumina_full.reference_fasta
File — Default: None
Reference genome to align reads to.

sarscov2_illumina_full.sra_title
String — Default: None
???

Other inputs¶

Show/Hide

sarscov2_illumina_full.assemble_refbased.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.assemble_refbased.align_to_ref.machine_mem_gb
Int? — Default: None
???

sarscov2_illumina_full.assemble_refbased.align_to_ref.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

sarscov2_illumina_full.assemble_refbased.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.assemble_refbased.align_to_self.machine_mem_gb
Int? — Default: None
???

sarscov2_illumina_full.assemble_refbased.align_to_self.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

sarscov2_illumina_full.assemble_refbased.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

sarscov2_illumina_full.assemble_refbased.call_consensus.machine_mem_gb
Int? — Default: None
???

sarscov2_illumina_full.assemble_refbased.call_consensus.major_cutoff
Float? — Default: 0.5
If the major allele is present at a frequency higher than this cutoff, we will call an unambiguous base at that position. If it is equal to or below this cutoff, we will call an ambiguous base representing all possible alleles at that position.

sarscov2_illumina_full.assemble_refbased.call_consensus.mark_duplicates
Boolean? — Default: false
???

sarscov2_illumina_full.assemble_refbased.ivar_trim.docker
String — Default: "andersenlabapps/ivar:1.3"
???

sarscov2_illumina_full.assemble_refbased.ivar_trim.machine_mem_gb
Int? — Default: None
???

sarscov2_illumina_full.assemble_refbased.ivar_trim.min_keep_length
Int? — Default: None
Minimum length of read to retain after trimming (Default: 30)

sarscov2_illumina_full.assemble_refbased.ivar_trim.min_quality
Int? — Default: 1
Minimum quality threshold for sliding window to pass (Default: 20)

sarscov2_illumina_full.assemble_refbased.ivar_trim.sliding_window
Int? — Default: None
Width of sliding window for quality trimming (Default: 4)

sarscov2_illumina_full.assemble_refbased.merge_align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.assemble_refbased.merge_align_to_ref.reheader_table
File? — Default: None
???

sarscov2_illumina_full.assemble_refbased.merge_align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.assemble_refbased.merge_align_to_self.reheader_table
File? — Default: None
???

sarscov2_illumina_full.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.

sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.bin_large_plots
Boolean — Default: false
???

sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.binning_summary_statistic
String? — Default: "max"
???

sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.plot_only_non_duplicates
Boolean — Default: false
???

sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.skip_mark_dupes
Boolean — Default: false
???

sarscov2_illumina_full.assemble_refbased.plot_self_coverage.bin_large_plots
Boolean — Default: false
???

sarscov2_illumina_full.assemble_refbased.plot_self_coverage.binning_summary_statistic
String? — Default: "max"
???

sarscov2_illumina_full.assemble_refbased.plot_self_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.assemble_refbased.plot_self_coverage.plot_only_non_duplicates
Boolean — Default: false
???

sarscov2_illumina_full.assemble_refbased.plot_self_coverage.skip_mark_dupes
Boolean — Default: false
???

sarscov2_illumina_full.assemble_refbased.run_discordance.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.biosample_merge.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.biosample_to_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

sarscov2_illumina_full.demux_deplete.blastDbs
Array[File]? — Default: None
???

sarscov2_illumina_full.demux_deplete.bmtaggerDbs
Array[File]? — Default: None
???

sarscov2_illumina_full.demux_deplete.bwaDbs
Array[File]? — Default: None
???

sarscov2_illumina_full.demux_deplete.default_filename_keys
Array[String] — Default: ["spike_in"]
???

sarscov2_illumina_full.demux_deplete.default_sample_keys
Array[String] — Default: ["amplicon_set", "control"]
???

sarscov2_illumina_full.demux_deplete.deplete.clear_tags
Boolean? — Default: false
???

sarscov2_illumina_full.demux_deplete.deplete.cpu
Int? — Default: 8
???

sarscov2_illumina_full.demux_deplete.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

sarscov2_illumina_full.demux_deplete.deplete.machine_mem_gb
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.deplete.query_chunk_size
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

sarscov2_illumina_full.demux_deplete.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.demux_deplete.illumina_demux.flowcell
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.forceGC
Boolean? — Default: true
???

sarscov2_illumina_full.demux_deplete.illumina_demux.machine_mem_gb
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.maxMismatches
Int? — Default: 0
???

sarscov2_illumina_full.demux_deplete.illumina_demux.maxNoCalls
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.maxReadsInRamPerTile
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.maxRecordsInRam
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.minimumBaseQuality
Int? — Default: 10
???

sarscov2_illumina_full.demux_deplete.illumina_demux.minimumQuality
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.minMismatchDelta
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.readStructure
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.runinfo
File? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.runStartDate
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.sequencingCenter
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.illumina_demux.threads
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.min_reads_per_bam
Int — Default: 100
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.comment
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.config
File? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.config_yaml
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.data_dir
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.exclude_modules
Array[String]? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.export
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.flat
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.force
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.full_names
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.ignore_analysis_files
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.ignore_sample_names
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.interactive
Boolean — Default: true
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.lint
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.megaQC_upload
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.module_to_use
Array[String]? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.no_data_dir
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.out_dir
String — Default: "./multiqc-output"
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.pdf
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.sample_names
File? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.tag
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.template
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.title
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_cleaned.zip_data_dir
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.comment
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.config
File? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.config_yaml
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.data_dir
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.exclude_modules
Array[String]? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.export
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.flat
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.force
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.full_names
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.ignore_analysis_files
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.ignore_sample_names
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.interactive
Boolean — Default: true
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.lint
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.megaQC_upload
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.module_to_use
Array[String]? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.no_data_dir
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.out_dir
String — Default: "./multiqc-output"
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

sarscov2_illumina_full.demux_deplete.multiqc_raw.pdf
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.sample_names
File? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.tag
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.template
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.title
String? — Default: None
???

sarscov2_illumina_full.demux_deplete.multiqc_raw.zip_data_dir
Boolean — Default: false
???

sarscov2_illumina_full.demux_deplete.sample_rename_map
File? — Default: None
If 'samples' need to be renamed, provide a two-column tsv that contains at least the following columns: internal_id, external_id. All samples will be renamed prior to analysis. Any samples described in the samplesheets that are not present in sample_rename_map will be unaltered. If this is omitted, no samples will be renamed.

sarscov2_illumina_full.demux_deplete.samplesheet_rename_ids.new_id_col
String — Default: 'external_id'
???

sarscov2_illumina_full.demux_deplete.samplesheet_rename_ids.old_id_col
String — Default: 'internal_id'
???

sarscov2_illumina_full.demux_deplete.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.demux_deplete.spike_summary.output_prefix
String — Default: "count_summary"
???

sarscov2_illumina_full.demux_deplete.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.demux_deplete.spikein.machine_mem_gb
Int? — Default: None
???

sarscov2_illumina_full.demux_deplete.spikein.topNHits
Int — Default: 3
???

sarscov2_illumina_full.demux_deplete.sra_meta_prep.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.gisaid_meta_prep.authors
String? — Default: None
???

sarscov2_illumina_full.gisaid_meta_prep.continent
String — Default: "North America"
???

sarscov2_illumina_full.gisaid_meta_prep.originating_lab_addr
String? — Default: None
???

sarscov2_illumina_full.gisaid_meta_prep.strict
Boolean — Default: true
???

sarscov2_illumina_full.gisaid_meta_prep.submitting_lab_addr
String? — Default: None
???

sarscov2_illumina_full.gisaid_meta_prep.submitting_lab_name
String? — Default: None
???

sarscov2_illumina_full.gisaid_meta_prep.username
String? — Default: None
???

sarscov2_illumina_full.min_genome_bases
Int — Default: 15000
???

sarscov2_illumina_full.ntc_max.default_empty
Int — Default: 0
???

sarscov2_illumina_full.package_genbank_ftp_submission.docker
String — Default: "quay.io/broadinstitute/viral-baseimage:0.1.20"
???

sarscov2_illumina_full.rename_fasta_header.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.rename_fasta_header.out_basename
String — Default: basename(genome_fasta,".fasta")
???

sarscov2_illumina_full.sarscov2_lineages.nextclade_one_sample.auspice_reference_tree_json
File? — Default: None
???

sarscov2_illumina_full.sarscov2_lineages.nextclade_one_sample.gene_annotations_json
File? — Default: None
???

sarscov2_illumina_full.sarscov2_lineages.nextclade_one_sample.pcr_primers_csv
File? — Default: None
???

sarscov2_illumina_full.sarscov2_lineages.nextclade_one_sample.qc_config_json
File? — Default: None
???

sarscov2_illumina_full.sarscov2_lineages.nextclade_one_sample.root_sequence
File? — Default: None
???

sarscov2_illumina_full.sarscov2_lineages.pangolin_one_sample.include_putative
Boolean — Default: true
???

sarscov2_illumina_full.sarscov2_lineages.pangolin_one_sample.max_ambig
Float? — Default: None
???

sarscov2_illumina_full.sarscov2_lineages.pangolin_one_sample.min_length
Int? — Default: None
???

sarscov2_illumina_full.structured_comments.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_illumina_full.submit_genomes.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

sarscov2_illumina_full.vadr.docker
String — Default: "staphb/vadr:1.1.2"
???

sarscov2_illumina_full.vadr.vadr_opts
String — Default: "-s -r --nomisc --mkey NC_045512 --lowsim5term 2 --lowsim3term 2 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf"
???

sarscov2_lineages¶

Call Nextclade and Pangolin lineages on a single SARS-CoV-2 genome

Inputs¶

Required inputs¶

sarscov2_lineages.genome_fasta
File — Default: None
???

Other inputs¶

Show/Hide

sarscov2_lineages.nextclade_one_sample.auspice_reference_tree_json
File? — Default: None
???

sarscov2_lineages.nextclade_one_sample.gene_annotations_json
File? — Default: None
???

sarscov2_lineages.nextclade_one_sample.pcr_primers_csv
File? — Default: None
???

sarscov2_lineages.nextclade_one_sample.qc_config_json
File? — Default: None
???

sarscov2_lineages.nextclade_one_sample.root_sequence
File? — Default: None
???

sarscov2_lineages.pangolin_one_sample.include_putative
Boolean — Default: true
???

sarscov2_lineages.pangolin_one_sample.max_ambig
Float? — Default: None
???

sarscov2_lineages.pangolin_one_sample.min_length
Int? — Default: None
???

sarscov2_nextclade_multi¶

Create Nextclade visualizations on many SARS-CoV-2 genomes

Inputs¶

Required inputs¶

sarscov2_nextclade_multi.genome_fastas
Array[File]+ — Default: None
???

sarscov2_nextclade_multi.nextclade_many_samples.basename
String — Default: None
???

Other inputs¶

Show/Hide

sarscov2_nextclade_multi.nextclade_many_samples.auspice_reference_tree_json
File? — Default: None
???

sarscov2_nextclade_multi.nextclade_many_samples.gene_annotations_json
File? — Default: None
???

sarscov2_nextclade_multi.nextclade_many_samples.pcr_primers_csv
File? — Default: None
???

sarscov2_nextclade_multi.nextclade_many_samples.qc_config_json
File? — Default: None
???

sarscov2_nextclade_multi.nextclade_many_samples.root_sequence
File? — Default: None
???

sarscov2_sra_to_genbank¶

Full SARS-CoV-2 analysis workflow starting from SRA data and metadata and performing assembly, spike-in analysis, qc, lineage assignment, and packaging assemblies for data release.

Inputs¶

Required inputs¶

sarscov2_sra_to_genbank.amplicon_bed_default
File — Default: None
Amplicon primers to trim in reference coordinate space (0-based BED format). Will only be used if the SRA Experiment Design has a Library Strategy set to AMPLICON (will be ignored on all other values).

sarscov2_sra_to_genbank.package_genbank_ftp_submission.account_name
String — Default: None
???

sarscov2_sra_to_genbank.package_genbank_ftp_submission.author_template_sbt
File — Default: None
???

sarscov2_sra_to_genbank.package_genbank_ftp_submission.spuid_namespace
String — Default: None
???

sarscov2_sra_to_genbank.package_genbank_ftp_submission.submission_name
String — Default: None
???

sarscov2_sra_to_genbank.package_genbank_ftp_submission.submission_uid
String — Default: None
???

sarscov2_sra_to_genbank.reference_fasta
File — Default: None
Reference genome to align reads to.

sarscov2_sra_to_genbank.spikein_db
File — Default: None
???

sarscov2_sra_to_genbank.SRA_accessions
Array[String] — Default: None
SRA Run accession numbers (SRR####).

Other inputs¶

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sarscov2_sra_to_genbank.assemble_refbased.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.assemble_refbased.align_to_ref.machine_mem_gb
Int? — Default: None
???

sarscov2_sra_to_genbank.assemble_refbased.align_to_ref.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

sarscov2_sra_to_genbank.assemble_refbased.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.assemble_refbased.align_to_self.machine_mem_gb
Int? — Default: None
???

sarscov2_sra_to_genbank.assemble_refbased.align_to_self.sample_name
String — Default: basename(basename(basename(reads_unmapped_bam,".bam"),".taxfilt"),".clean")
???

sarscov2_sra_to_genbank.assemble_refbased.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

sarscov2_sra_to_genbank.assemble_refbased.call_consensus.machine_mem_gb
Int? — Default: None
???

sarscov2_sra_to_genbank.assemble_refbased.call_consensus.major_cutoff
Float? — Default: 0.5
If the major allele is present at a frequency higher than this cutoff, we will call an unambiguous base at that position. If it is equal to or below this cutoff, we will call an ambiguous base representing all possible alleles at that position.

sarscov2_sra_to_genbank.assemble_refbased.call_consensus.mark_duplicates
Boolean? — Default: false
???

sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.docker
String — Default: "andersenlabapps/ivar:1.3"
???

sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.machine_mem_gb
Int? — Default: None
???

sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.min_keep_length
Int? — Default: None
Minimum length of read to retain after trimming (Default: 30)

sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.min_quality
Int? — Default: 1
Minimum quality threshold for sliding window to pass (Default: 20)

sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.sliding_window
Int? — Default: None
Width of sliding window for quality trimming (Default: 4)

sarscov2_sra_to_genbank.assemble_refbased.merge_align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.assemble_refbased.merge_align_to_ref.reheader_table
File? — Default: None
???

sarscov2_sra_to_genbank.assemble_refbased.merge_align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.assemble_refbased.merge_align_to_self.reheader_table
File? — Default: None
???

sarscov2_sra_to_genbank.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.

sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.bin_large_plots
Boolean — Default: false
???

sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.binning_summary_statistic
String? — Default: "max"
???

sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.plot_only_non_duplicates
Boolean — Default: false
???

sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.skip_mark_dupes
Boolean — Default: false
???

sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.bin_large_plots
Boolean — Default: false
???

sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.binning_summary_statistic
String? — Default: "max"
???

sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.plot_only_non_duplicates
Boolean — Default: false
???

sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.skip_mark_dupes
Boolean — Default: false
???

sarscov2_sra_to_genbank.assemble_refbased.run_discordance.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.biosample_to_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.16.0"
???

sarscov2_sra_to_genbank.fastqc.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.Fetch_SRA_to_BAM.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.1"
???

sarscov2_sra_to_genbank.Fetch_SRA_to_BAM.machine_mem_gb
Int? — Default: None
???

sarscov2_sra_to_genbank.gisaid_meta_prep.authors
String? — Default: None
???

sarscov2_sra_to_genbank.gisaid_meta_prep.continent
String — Default: "North America"
???

sarscov2_sra_to_genbank.gisaid_meta_prep.fasta_filename
String? — Default: None
???

sarscov2_sra_to_genbank.gisaid_meta_prep.originating_lab_addr
String? — Default: None
???

sarscov2_sra_to_genbank.gisaid_meta_prep.submitting_lab_addr
String? — Default: None
???

sarscov2_sra_to_genbank.gisaid_meta_prep.submitting_lab_name
String? — Default: None
???

sarscov2_sra_to_genbank.gisaid_meta_prep.username
String? — Default: None
???

sarscov2_sra_to_genbank.min_genome_bases
Int — Default: 15000
???

sarscov2_sra_to_genbank.min_reads_per_bam
Int — Default: 100
???

sarscov2_sra_to_genbank.multiqc_raw.comment
String? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.config
File? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.config_yaml
String? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.data_dir
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

sarscov2_sra_to_genbank.multiqc_raw.exclude_modules
Array[String]? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.export
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.flat
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.force
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.full_names
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.ignore_analysis_files
String? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.ignore_sample_names
String? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.interactive
Boolean — Default: true
???

sarscov2_sra_to_genbank.multiqc_raw.lint
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.megaQC_upload
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.module_to_use
Array[String]? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.no_data_dir
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.out_dir
String — Default: "./multiqc-output"
???

sarscov2_sra_to_genbank.multiqc_raw.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

sarscov2_sra_to_genbank.multiqc_raw.pdf
Boolean — Default: false
???

sarscov2_sra_to_genbank.multiqc_raw.sample_names
File? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.tag
String? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.template
String? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.title
String? — Default: None
???

sarscov2_sra_to_genbank.multiqc_raw.zip_data_dir
Boolean — Default: false
???

sarscov2_sra_to_genbank.package_genbank_ftp_submission.docker
String — Default: "quay.io/broadinstitute/viral-baseimage:0.1.20"
???

sarscov2_sra_to_genbank.prefix_gisaid.out_basename
String — Default: basename(genome_fasta,".fasta")
???

sarscov2_sra_to_genbank.rename_fasta_header.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.rename_fasta_header.out_basename
String — Default: basename(genome_fasta,".fasta")
???

sarscov2_sra_to_genbank.sarscov2_lineages.nextclade_one_sample.auspice_reference_tree_json
File? — Default: None
???

sarscov2_sra_to_genbank.sarscov2_lineages.nextclade_one_sample.gene_annotations_json
File? — Default: None
???

sarscov2_sra_to_genbank.sarscov2_lineages.nextclade_one_sample.pcr_primers_csv
File? — Default: None
???

sarscov2_sra_to_genbank.sarscov2_lineages.nextclade_one_sample.qc_config_json
File? — Default: None
???

sarscov2_sra_to_genbank.sarscov2_lineages.nextclade_one_sample.root_sequence
File? — Default: None
???

sarscov2_sra_to_genbank.sarscov2_lineages.pangolin_one_sample.include_putative
Boolean — Default: true
???

sarscov2_sra_to_genbank.sarscov2_lineages.pangolin_one_sample.max_ambig
Float? — Default: None
???

sarscov2_sra_to_genbank.sarscov2_lineages.pangolin_one_sample.min_length
Int? — Default: None
???

sarscov2_sra_to_genbank.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.spike_summary.output_prefix
String — Default: "count_summary"
???

sarscov2_sra_to_genbank.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.spikein.machine_mem_gb
Int? — Default: None
???

sarscov2_sra_to_genbank.spikein.topNHits
Int — Default: 3
???

sarscov2_sra_to_genbank.structured_comments.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_sra_to_genbank.vadr.docker
String — Default: "staphb/vadr:1.1.2"
???

sarscov2_sra_to_genbank.vadr.vadr_opts
String — Default: "-s -r --nomisc --mkey NC_045512 --lowsim5term 2 --lowsim3term 2 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf"
???

scaffold_and_refine¶

Scaffold de novo contigs against a set of possible references and subsequently polish with reads.

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¶

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scaffold_and_refine.refine_2x_and_plot.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

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:2.1.16.1"
???

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(contigs_fasta,".fasta"),".assembly1-spades")
???

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

subsample_by_metadata¶

Filter and subsample a sequence set. See https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/filter.html

Inputs¶

Required inputs¶

subsample_by_metadata.filter_subsample_sequences.sample_metadata_tsv
File — Default: None
Metadata in tab-separated text format. See https://nextstrain-augur.readthedocs.io/en/stable/faq/metadata.html for details.

subsample_by_metadata.filter_subsample_sequences.sequences_fasta
File — Default: None
Set of sequences (unaligned fasta or aligned fasta -- one sequence per genome) or variants (vcf format) to subsample using augur filter.

Other inputs¶

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subsample_by_metadata.filter_subsample_sequences.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

subsample_by_metadata.filter_subsample_sequences.exclude
File? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.exclude_where
Array[String]? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.group_by
String? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.include
File? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.include_where
Array[String]? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.max_date
Float? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.min_date
Float? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.min_length
Int? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.non_nucleotide
Boolean — Default: true
???

subsample_by_metadata.filter_subsample_sequences.priority
File? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.sequences_per_group
Int? — Default: None
???

subsample_by_metadata.filter_subsample_sequences.subsample_seed
Int? — Default: None
???

subsample_by_metadata_with_focal¶

Filter and subsample a global sequence set with a bias towards a geographic area of interest.

Inputs¶

Required inputs¶

subsample_by_metadata_with_focal.sample_metadata_tsvs
Array[File]+ — Default: None
Tab-separated metadata file that contain binning variables and values. Must contain all samples: output will be filtered to the IDs present in this file.

subsample_by_metadata_with_focal.sequences_fasta
File — Default: None
Sequences in fasta format.

Other inputs¶

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subsample_by_metadata_with_focal.derived_cols.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

subsample_by_metadata_with_focal.derived_cols.lab_highlight_loc
String? — Default: None
???

subsample_by_metadata_with_focal.derived_cols.table_map
Array[File] — Default: []
???

subsample_by_metadata_with_focal.focal_bin_max
Int — Default: 50
The output will contain no more than this number of focal samples from each discrete value in the focal_bin_variable column.

subsample_by_metadata_with_focal.focal_bin_variable
String — Default: "division"
The focal subset of samples will be evenly subsampled across the discrete values of this column header.

subsample_by_metadata_with_focal.focal_value
String — Default: "North America"
The dataset will be bifurcated based whether the focal_variable column matches this value or not. Rows that match this value are considered to be part of the 'focal' set of interest, rows that do not are part of the 'global' set.

subsample_by_metadata_with_focal.focal_variable
String — Default: "region"
The dataset will be bifurcated based on this column header.

subsample_by_metadata_with_focal.global_bin_max
Int — Default: 50
The output will contain no more than this number of global samples from each discrete value in the global_bin_variable column.

subsample_by_metadata_with_focal.global_bin_variable
String — Default: "country"
The global subset of samples will be evenly subsampled across the discrete values of this column header.

subsample_by_metadata_with_focal.prefilter.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

subsample_by_metadata_with_focal.prefilter.exclude
File? — Default: None
???

subsample_by_metadata_with_focal.prefilter.exclude_where
Array[String]? — Default: None
???

subsample_by_metadata_with_focal.prefilter.group_by
String? — Default: None
???

subsample_by_metadata_with_focal.prefilter.include
File? — Default: None
???

subsample_by_metadata_with_focal.prefilter.include_where
Array[String]? — Default: None
???

subsample_by_metadata_with_focal.prefilter.max_date
Float? — Default: None
???

subsample_by_metadata_with_focal.prefilter.min_date
Float? — Default: None
???

subsample_by_metadata_with_focal.prefilter.min_length
Int? — Default: None
???

subsample_by_metadata_with_focal.prefilter.non_nucleotide
Boolean — Default: true
???

subsample_by_metadata_with_focal.prefilter.priority
File? — Default: None
???

subsample_by_metadata_with_focal.prefilter.sequences_per_group
Int? — Default: None
???

subsample_by_metadata_with_focal.prefilter.subsample_seed
Int? — Default: None
???

subsample_by_metadata_with_focal.priorities
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

subsample_by_metadata_with_focal.subsample_focal.exclude
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.include
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.include_where
Array[String]? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.max_date
Float? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.min_date
Float? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.min_length
Int? — Default: None
???

subsample_by_metadata_with_focal.subsample_focal.non_nucleotide
Boolean — Default: true
???

subsample_by_metadata_with_focal.subsample_focal.subsample_seed
Int? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.docker
String — Default: "nextstrain/base:build-20201214T004216Z"
???

subsample_by_metadata_with_focal.subsample_global.exclude
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.include
File? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.include_where
Array[String]? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.max_date
Float? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.min_date
Float? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.min_length
Int? — Default: None
???

subsample_by_metadata_with_focal.subsample_global.non_nucleotide
Boolean — Default: true
???

subsample_by_metadata_with_focal.subsample_global.subsample_seed
Int? — Default: None
???

subsample_by_metadata_with_focal.tsv_join.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

trimal¶

Trim a multiple sequence alignment with Trimal.

Inputs¶

Required inputs¶

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

Other inputs¶

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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
???