4.48. 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.

4.48.1. Inputs

4.48.1.1. 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
???

4.48.1.2. Other inputs

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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:1.3.1"
???

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_to_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.19.1"
???

sarscov2_illumina_full.biosample_to_genbank.s_dropout_note
Boolean — Default: true
???

sarscov2_illumina_full.data_tables.docker
String — Default: "schaluvadi/pathogen-genomic-surveillance:api-wdl"
???

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.max_vadr_alerts
Int — Default: 0
???

sarscov2_illumina_full.min_genome_bases
Int — Default: 15000
???

sarscov2_illumina_full.nextclade_many_samples.auspice_reference_tree_json
File? — Default: None
???

sarscov2_illumina_full.nextclade_many_samples.gene_annotations_json
File? — Default: None
???

sarscov2_illumina_full.nextclade_many_samples.pcr_primers_csv
File? — Default: None
???

sarscov2_illumina_full.nextclade_many_samples.qc_config_json
File? — Default: None
???

sarscov2_illumina_full.nextclade_many_samples.root_sequence
File? — Default: None
???

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.docker
String — Default: "staphb/pangolin:2.3.2-pangolearn-2021-02-21"
???

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-20210127T135203Z"
???

sarscov2_illumina_full.terra_project
String? — Default: None
???

sarscov2_illumina_full.vadr.docker
String — Default: "staphb/vadr:1.1.3"
???

sarscov2_illumina_full.vadr.vadr_opts
String — Default: "-s -r --nomisc --mkey NC_045512 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf,insertnn,deletinn"
???

sarscov2_illumina_full.workspace_name
String? — Default: None
???

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