4.61. 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.
4.61.1. Inputs¶
4.61.1.1. 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
Synthetic sequences (e.g. ERCC, SDSI) that are used to track potential contamination within sequencing plate processing.
sarscov2_illumina_full.flowcell_tgz
File — Default: None
???
sarscov2_illumina_full.gisaid_meta_prep.submitting_lab_name
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.sarscov2_biosample_load.bioproject
String — Default: None
???
sarscov2_illumina_full.sarscov2_biosample_load.ftp_config_js
File — Default: None
???
sarscov2_illumina_full.sarscov2_biosample_load.id_salt
File — Default: None
???
sarscov2_illumina_full.sra_title
String — Default: None
???
4.61.1.2. Advanced inputs¶
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sarscov2_illumina_full.assemble_refbased.call_consensus.mark_duplicates
Boolean — Default: false
Instead of removing duplicates, simply marks them.
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.demux_deplete.bmtaggerDbs
Array[File]? — Default: None
Tool that can discriminate between human and bacterial reads and other reads by using short fragments. Databases must be provided to onset depletion.Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.
sarscov2_illumina_full.demux_deplete.illumina_demux.runinfo
File? — Default: None
if we are overriding the RunInfo file, use the path of the file provided. Otherwise the default will be RunInfo.xml.
sarscov2_illumina_full.demux_deplete.sort_reads
Boolean — Default: true
Output bam files will be sorted by read name.
4.61.1.3. Other inputs¶
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sarscov2_illumina_full.accessioned_samples.drop_empty
Boolean — Default: true
???
sarscov2_illumina_full.accessioned_samples.drop_header
Boolean — Default: true
???
sarscov2_illumina_full.accessioned_samples.out_name
String — Default: "~{basename(basename(tsv,'.txt'),'.tsv')}-~{col}.txt"
???
sarscov2_illumina_full.assemble_refbased.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
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_ref_options
Map[String,String] — Default: {"novoalign": "-r Random -l 40 -g 40 -x 20 -t 501 -k", "bwa": "-k 12 -B 1", "minimap2": ""}
???
sarscov2_illumina_full.assemble_refbased.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
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.align_to_self_options
Map[String,String] — Default: {"novoalign": "-r Random -l 40 -g 40 -x 20 -t 100", "bwa": "", "minimap2": ""}
???
sarscov2_illumina_full.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).
sarscov2_illumina_full.assemble_refbased.alignment_metrics.amplicon_set
String? — Default: None
???
sarscov2_illumina_full.assemble_refbased.alignment_metrics.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.assemble_refbased.alignment_metrics.machine_mem_gb
Int? — Default: None
???
sarscov2_illumina_full.assemble_refbased.alignment_metrics.max_amp_len
Int? — Default: 5000
???
sarscov2_illumina_full.assemble_refbased.alignment_metrics.max_amplicons
Int? — Default: 500
???
sarscov2_illumina_full.assemble_refbased.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.33.0"
???
sarscov2_illumina_full.assemble_refbased.call_consensus.machine_mem_gb
Int? — Default: None
???
sarscov2_illumina_full.assemble_refbased.isnvs_ref.docker
String — Default: "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
???
sarscov2_illumina_full.assemble_refbased.isnvs_ref.out_basename
String — Default: basename(aligned_bam,'.bam')
???
sarscov2_illumina_full.assemble_refbased.isnvs_self.docker
String — Default: "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
???
sarscov2_illumina_full.assemble_refbased.isnvs_self.out_basename
String — Default: basename(aligned_bam,'.bam')
???
sarscov2_illumina_full.assemble_refbased.ivar_trim.bam_basename
String — Default: basename(aligned_bam,".bam")
???
sarscov2_illumina_full.assemble_refbased.ivar_trim.disk_size
Int — Default: 375
???
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.primer_offset
Int? — Default: None
???
sarscov2_illumina_full.assemble_refbased.merge_align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
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:2.1.33"
???
sarscov2_illumina_full.assemble_refbased.merge_align_to_self.reheader_table
File? — Default: None
???
sarscov2_illumina_full.assemble_refbased.novocraft_license
File? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.base_q_threshold
Int? — Default: None
???
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:2.1.33"
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.mapping_q_threshold
Int? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.max_coverage_depth
Int? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.plot_height_pixels
Int? — Default: 850
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.plot_only_non_duplicates
Boolean — Default: false
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.plot_pixels_per_inch
Int? — Default: 100
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.plot_width_pixels
Int? — Default: 1100
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.plotXLimits
String? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.plotYLimits
String? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.read_length_threshold
Int? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_ref_coverage.skip_mark_dupes
Boolean — Default: false
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.base_q_threshold
Int? — Default: None
???
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:2.1.33"
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.mapping_q_threshold
Int? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.max_coverage_depth
Int? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.plot_height_pixels
Int? — Default: 850
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.plot_only_non_duplicates
Boolean — Default: false
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.plot_pixels_per_inch
Int? — Default: 100
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.plot_width_pixels
Int? — Default: 1100
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.plotXLimits
String? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.plotYLimits
String? — Default: None
???
sarscov2_illumina_full.assemble_refbased.plot_self_coverage.read_length_threshold
Int? — Default: None
???
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:2.1.33"
???
sarscov2_illumina_full.assembly_meta_tsv.cpus
Int — Default: 4
???
sarscov2_illumina_full.biosample_merge.machine_mem_gb
Int — Default: 7
???
sarscov2_illumina_full.biosample_merge.out_suffix
String — Default: ".txt"
???
sarscov2_illumina_full.biosample_merge.prefer_first
Boolean — Default: true
???
sarscov2_illumina_full.biosample_to_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???
sarscov2_illumina_full.biosample_to_genbank.s_dropout_note
Boolean — Default: true
???
sarscov2_illumina_full.collab_ids_tsv
File? — Default: None
???
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.bwaDbs
Array[File]? — Default: None
???
sarscov2_illumina_full.demux_deplete.default_filename_keys
Array[String] — Default: ["spike_in", "batch_lib"]
???
sarscov2_illumina_full.demux_deplete.default_sample_keys
Array[String] — Default: ["amplicon_set", "control", "batch_lib", "viral_ct"]
???
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:2.1.33.0"
???
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.disk_size
Int — Default: 2625
???
sarscov2_illumina_full.demux_deplete.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.demux_deplete.illumina_demux.flowcell
String? — Default: None
???
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.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.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.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:2.1.33"
???
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:2.1.33"
???
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:2.1.33"
???
sarscov2_illumina_full.download_entities_tsv.docker
String — Default: "schaluvadi/pathogen-genomic-surveillance:api-wdl"
???
sarscov2_illumina_full.download_entities_tsv.outname
String — Default: "~{terra_project}-~{workspace_name}-~{table_name}.tsv"
???
sarscov2_illumina_full.filter_bad_ntc_batches.genome_status_json
File? — Default: None
???
sarscov2_illumina_full.gcs_out_cdc
String? — Default: None
???
sarscov2_illumina_full.gcs_out_metrics
String? — Default: None
???
sarscov2_illumina_full.gcs_out_sra
String? — Default: None
???
sarscov2_illumina_full.gisaid_meta_prep.address_map
String — Default: '{}'
???
sarscov2_illumina_full.gisaid_meta_prep.authors_map
String — Default: '{}'
???
sarscov2_illumina_full.gisaid_meta_prep.continent
String — Default: "North America"
???
sarscov2_illumina_full.gisaid_meta_prep.strict
Boolean — Default: true
???
sarscov2_illumina_full.gisaid_meta_prep.username
String? — Default: None
???
sarscov2_illumina_full.instrument_model
String? — Default: None
???
sarscov2_illumina_full.ivar_trim_stats.docker
String — Default: "quay.io/broadinstitute/py3-bio:0.1.2"
???
sarscov2_illumina_full.max_vadr_alerts
Int — Default: 0
???
sarscov2_illumina_full.min_genome_bases
Int — Default: 24000
???
sarscov2_illumina_full.min_genome_coverage
Int? — Default: None
???
sarscov2_illumina_full.ntc_max.default_empty
Int — Default: 0
???
sarscov2_illumina_full.ntc_max_unambig
Int — Default: 3000
???
sarscov2_illumina_full.package_genbank_ftp_submission.docker
String — Default: "quay.io/broadinstitute/viral-baseimage:0.1.20"
???
sarscov2_illumina_full.passing_cat.disk_size
Int — Default: 750
???
sarscov2_illumina_full.passing_cat.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.passing_cat_prefilter.cpus
Int — Default: 4
???
sarscov2_illumina_full.passing_ntc.disk_size
Int — Default: 750
???
sarscov2_illumina_full.passing_ntc.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.passing_ntc.out_fname
String — Default: sub(sub(basename(sequences,".zst"),".vcf",".filtered.vcf"),".fasta$",".filtered.fasta")
???
sarscov2_illumina_full.picard_alignment_merge.machine_mem_gb
Int — Default: 7
???
sarscov2_illumina_full.picard_alignment_merge.out_suffix
String — Default: ".txt"
???
sarscov2_illumina_full.picard_alignment_merge.prefer_first
Boolean — Default: true
???
sarscov2_illumina_full.picard_insertsize_merge.machine_mem_gb
Int — Default: 7
???
sarscov2_illumina_full.picard_insertsize_merge.out_suffix
String — Default: ".txt"
???
sarscov2_illumina_full.picard_insertsize_merge.prefer_first
Boolean — Default: true
???
sarscov2_illumina_full.picard_wgs_merge.machine_mem_gb
Int — Default: 7
???
sarscov2_illumina_full.picard_wgs_merge.out_suffix
String — Default: ".txt"
???
sarscov2_illumina_full.picard_wgs_merge.prefer_first
Boolean — Default: true
???
sarscov2_illumina_full.read_structure
String? — Default: None
???
sarscov2_illumina_full.rename_fasta_header.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.rename_fasta_header.out_basename
String — Default: basename(genome_fasta,".fasta")
???
sarscov2_illumina_full.sample_rename_map
File? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.filter_sequences_by_length.disk_size
Int — Default: 750
???
sarscov2_illumina_full.sarscov2_batch_relineage.filter_sequences_by_length.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.sarscov2_batch_relineage.merge_annotated.machine_mem_gb
Int — Default: 7
???
sarscov2_illumina_full.sarscov2_batch_relineage.merge_annotated.prefer_first
Boolean — Default: true
???
sarscov2_illumina_full.sarscov2_batch_relineage.merge_raw.machine_mem_gb
Int — Default: 7
???
sarscov2_illumina_full.sarscov2_batch_relineage.merge_raw.prefer_first
Boolean — Default: true
???
sarscov2_illumina_full.sarscov2_batch_relineage.nextclade_many_samples.auspice_reference_tree_json
File? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.nextclade_many_samples.disk_size
Int — Default: 150
???
sarscov2_illumina_full.sarscov2_batch_relineage.nextclade_many_samples.docker
String — Default: "nextstrain/nextclade:2.12.0"
???
sarscov2_illumina_full.sarscov2_batch_relineage.nextclade_many_samples.gene_annotations_json
File? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.nextclade_many_samples.pcr_primers_csv
File? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.nextclade_many_samples.qc_config_json
File? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.nextclade_many_samples.root_sequence
File? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.nextclade_many_samples.virus_properties
File? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.pangolin_many_samples.analysis_mode
String? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.pangolin_many_samples.docker
String — Default: "quay.io/staphb/pangolin:4.3.1-pdata-1.22"
???
sarscov2_illumina_full.sarscov2_batch_relineage.pangolin_many_samples.max_ambig
Float? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.pangolin_many_samples.min_length
Int? — Default: None
???
sarscov2_illumina_full.sarscov2_batch_relineage.pangolin_many_samples.update_dbs_now
Boolean — Default: false
???
sarscov2_illumina_full.sarscov2_batch_relineage.today.timezone
String? — Default: None
???
sarscov2_illumina_full.sarscov2_biosample_load.biosample_submit_tsv
File? — Default: None
???
sarscov2_illumina_full.sarscov2_biosample_load.biosample_submit_tsv_ftp_upload.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???
sarscov2_illumina_full.sarscov2_biosample_load.biosample_tsv_filter_preexisting.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???
sarscov2_illumina_full.sarscov2_biosample_load.crsp_meta_etl.allowed_purposes
String — Default: '["Baseline surveillance (random sampling)", "Targeted surveillance (non-random sampling)", "Screening for Variants of Concern (VOC)", "Longitudinal surveillance (repeat sampling of individuals)", "Vaccine escape surveillance", "Cluster/Outbreak investigation"]'
???
sarscov2_illumina_full.sarscov2_biosample_load.crsp_meta_etl.country
String — Default: 'USA'
???
sarscov2_illumina_full.sarscov2_biosample_load.crsp_meta_etl.docker
String — Default: "quay.io/broadinstitute/py3-bio:0.1.2"
???
sarscov2_illumina_full.sarscov2_biosample_load.crsp_meta_etl.ontology_map_body_part
String — Default: '{"AN SWAB": "Anterior Nares", "AN Swab": "Anterior Nares", "Anterior Nares": "Anterior Nares", "Swab": "Upper respiratory tract", "Viral": "Upper respiratory tract", "Null": "Anterior Nares", "NP Swab": "Nasopharynx (NP)", "Nasopharynx (NP)": "Nasopharynx (NP)", "Oropharynx (OP)": "Oropharynx (OP)", "Other": "Not Provided"}'
???
sarscov2_illumina_full.sarscov2_biosample_load.crsp_meta_etl.ontology_map_states
String — Default: '{"AL": "Alabama", "AK": "Alaska", "AZ": "Arizona", "AR": "Arkansas", "CA": "California", "CO": "Colorado", "CT": "Connecticut", "DE": "Delaware", "DC": "District of Columbia", "FL": "Florida", "GA": "Georgia", "HI": "Hawaii", "ID": "Idaho", "IL": "Illinois", "IN": "Indiana", "IA": "Iowa", "KS": "Kansas", "KY": "Kentucky", "LA": "Louisiana", "ME": "Maine", "MD": "Maryland", "MA": "Massachusetts", "MI": "Michigan", "MN": "Minnesota", "MS": "Mississippi", "MO": "Missouri", "MT": "Montana", "NE": "Nebraska", "NV": "Nevada", "NH": "New Hampshire", "NJ": "New Jersey", "NM": "New Mexico", "NY": "New York", "NC": "North Carolina", "ND": "North Dakota", "OH": "Ohio", "OK": "Oklahoma", "OR": "Oregon", "PA": "Pennsylvania", "RI": "Rhode Island", "SC": "South Carolina", "SD": "South Dakota", "TN": "Tennessee", "TX": "Texas", "UT": "Utah", "VT": "Vermont", "VA": "Virginia", "WA": "Washington", "WV": "West Virginia", "WI": "Wisconsin", "WY": "Wyoming"}'
???
sarscov2_illumina_full.sarscov2_biosample_load.crsp_meta_etl.org_name_map
String — Default: '{"Broad Institute Clinical Research Sequencing Platform": "Broad Institute Clinical Research Sequencing Platform", "Massachusetts General Hospital": "Massachusetts General Hospital", "RIDOH": "Rhode Island Department of Health", "BIOBOT": "Biobot Analytics", "FLOW":"Flow Health", "MESA":"Colorado Mesa University", "CAPTURE":"Capture Diagnostics Hawaii", "BUBMC":"Boston Medical Center", "UCF":"University of Central Florida"}'
???
sarscov2_illumina_full.sarscov2_biosample_load.crsp_meta_etl.prefix_map
String — Default: '{"Broad Institute Clinical Research Sequencing Platform": "CRSP_", "Massachusetts General Hospital": "MGH_", "Rhode Island Department of Health": "RIDOH_", "Biobot Analytics": "Biobot_", "Flow Health":"FlowHealth_", "Colorado Mesa University":"CMU_", "Capture Diagnostics Hawaii":"Capture_", "Boston Medical Center":"BMC_", "University of Central Florida":"UCF_"}'
???
sarscov2_illumina_full.sarscov2_biosample_load.crsp_meta_etl.sequencing_lab_prefix
String — Default: 'CDCBI'
???
sarscov2_illumina_full.sarscov2_biosample_load.prod_test
String — Default: "Production"
???
sarscov2_illumina_full.sarscov2_biosample_load.sample_meta_crsp
File? — Default: None
???
sarscov2_illumina_full.sarscov2_biosample_load.tsv_join.machine_mem_gb
Int — Default: 7
???
sarscov2_illumina_full.sarscov2_biosample_load.tsv_join.out_suffix
String — Default: ".txt"
???
sarscov2_illumina_full.sarscov2_biosample_load.tsv_join.prefer_first
Boolean — Default: true
???
sarscov2_illumina_full.sc2_meta_final.address_map
String — Default: '{}'
???
sarscov2_illumina_full.sc2_meta_final.authors_map
String — Default: '{}'
???
sarscov2_illumina_full.sc2_meta_final.collab_ids_addcols
Array[String] — Default: ['collaborator_id', 'hl7_message_id', 'matrix_id']
???
sarscov2_illumina_full.sc2_meta_final.collab_ids_idcol
String — Default: 'external_id'
???
sarscov2_illumina_full.sc2_meta_final.docker
String — Default: "quay.io/broadinstitute/py3-bio:0.1.2"
???
sarscov2_illumina_full.sc2_meta_final.filter_to_ids
File? — Default: None
???
sarscov2_illumina_full.sc2_meta_final.max_date
String? — Default: None
???
sarscov2_illumina_full.sc2_meta_final.min_date
String? — Default: None
???
sarscov2_illumina_full.sequencing_report.docker
String — Default: "quay.io/broadinstitute/sc2-rmd:0.1.25"
???
sarscov2_illumina_full.sequencing_report.intro_blurb
String — Default: "The Broad Institute Viral Genomics group, in partnership with the Genomics Platform and Data Sciences Platform, has been engaged in viral sequencing of COVID-19 patients since March 2020."
???
sarscov2_illumina_full.sequencing_report.machine_mem_gb
Int — Default: 7
???
sarscov2_illumina_full.sequencing_report.min_date
String? — Default: None
???
sarscov2_illumina_full.sequencing_report.sequencing_lab
String — Default: "Broad Institute"
???
sarscov2_illumina_full.sequencing_report.voc_list
String? — Default: None
???
sarscov2_illumina_full.sequencing_report.voi_list
String? — Default: None
???
sarscov2_illumina_full.structured_comments.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.submit_genomes.disk_size
Int — Default: 750
???
sarscov2_illumina_full.submit_genomes.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.submit_genomes.out_fname
String — Default: sub(sub(basename(sequences,".zst"),".vcf",".filtered.vcf"),".fasta$",".filtered.fasta")
???
sarscov2_illumina_full.submittable_filter.disk_size
Int — Default: 750
???
sarscov2_illumina_full.submittable_filter.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_illumina_full.submittable_filter.out_fname
String — Default: sub(sub(basename(sequences,".zst"),".vcf",".filtered.vcf"),".fasta$",".filtered.fasta")
???
sarscov2_illumina_full.terra_project
String? — Default: None
???
sarscov2_illumina_full.vadr.cpus
Int — Default: 2
???
sarscov2_illumina_full.vadr.docker
String — Default: "quay.io/staphb/vadr:1.5.1"
???
sarscov2_illumina_full.vadr.maxlen
Int — Default: 30000
???
sarscov2_illumina_full.vadr.mem_size
Int — Default: 4
???
sarscov2_illumina_full.vadr.minlen
Int — Default: 50
???
sarscov2_illumina_full.vadr.vadr_opts
String — Default: "--glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn"
???
sarscov2_illumina_full.workspace_name
String? — Default: None
???
4.61.2. Outputs¶
sarscov2_illumina_full.aligned_trimmed_bams
Array[File]
???
sarscov2_illumina_full.assembled_ids
Array[String]
???
sarscov2_illumina_full.assemblies_fasta
Array[File]
???
sarscov2_illumina_full.assembly_stats_final_relineage_tsv
File
???
sarscov2_illumina_full.assembly_stats_final_tsv
File
???
sarscov2_illumina_full.assembly_stats_relineage_tsv
File
???
sarscov2_illumina_full.assembly_stats_tsv
File
???
sarscov2_illumina_full.biosample_attributes_out
Array[File]
???
sarscov2_illumina_full.cleaned_bam_uris
File
???
sarscov2_illumina_full.cleaned_bams_tiny
Array[File]
???
sarscov2_illumina_full.cleaned_reads_unaligned_bams
Array[File]
???
sarscov2_illumina_full.data_tables_out
Array[String]
???
sarscov2_illumina_full.demux_commonBarcodes
Array[File]
???
sarscov2_illumina_full.demux_metrics
Array[File]
???
sarscov2_illumina_full.demux_outlierBarcodes
Array[File]
???
sarscov2_illumina_full.failed_annotation_ids
Array[String]
???
sarscov2_illumina_full.failed_assembly_ids
Array[String]
???
sarscov2_illumina_full.genbank_fasta
File
???
sarscov2_illumina_full.genbank_source_table
File
???
sarscov2_illumina_full.gisaid_fasta
File
???
sarscov2_illumina_full.gisaid_meta_csv
File
???
sarscov2_illumina_full.id_map_tsv
File?
???
sarscov2_illumina_full.ivar_trim_stats_html
File
???
sarscov2_illumina_full.ivar_trim_stats_png
File
???
sarscov2_illumina_full.ivar_trim_stats_tsv
File
???
sarscov2_illumina_full.max_ntc_bases
Int
???
sarscov2_illumina_full.meta_by_filename_json
File
???
sarscov2_illumina_full.multiqc_report_cleaned
File
???
sarscov2_illumina_full.multiqc_report_raw
File
???
sarscov2_illumina_full.nextalign_msa
File
???
sarscov2_illumina_full.nextclade_all_json
File
???
sarscov2_illumina_full.nextclade_all_tsv
File
???
sarscov2_illumina_full.nextclade_auspice_json
File
???
sarscov2_illumina_full.nextmeta_tsv
File
???
sarscov2_illumina_full.ntc_rejected_batches
Array[String]
???
sarscov2_illumina_full.ntc_rejected_lanes
Array[String]
???
sarscov2_illumina_full.num_assembled
Int
???
sarscov2_illumina_full.num_failed_annotation
Int
???
sarscov2_illumina_full.num_failed_assembly
Int
???
sarscov2_illumina_full.num_read_files
Int
???
sarscov2_illumina_full.num_samples
Int
???
sarscov2_illumina_full.num_submittable
Int
???
sarscov2_illumina_full.pangolin_msa
File
???
sarscov2_illumina_full.pangolin_report
File
???
sarscov2_illumina_full.passing_fasta
File
???
sarscov2_illumina_full.picard_metrics_alignment
File
???
sarscov2_illumina_full.picard_metrics_wgs
File
???
sarscov2_illumina_full.primer_trimmed_read_count
Array[Int]
???
sarscov2_illumina_full.primer_trimmed_read_percent
Array[Float]
???
sarscov2_illumina_full.raw_reads_unaligned_bams
Array[File]
???
sarscov2_illumina_full.read_counts_depleted
Array[Int]
???
sarscov2_illumina_full.read_counts_raw
Array[Int]
???
sarscov2_illumina_full.run_date
String
???
sarscov2_illumina_full.run_id
String
???
sarscov2_illumina_full.sequencing_reports
File?
???
sarscov2_illumina_full.spikein_counts
File
???
sarscov2_illumina_full.sra_metadata
File
???
sarscov2_illumina_full.submission_xml
File
???
sarscov2_illumina_full.submission_zip
File
???
sarscov2_illumina_full.submit_ready
File
???
sarscov2_illumina_full.submittable_ids
Array[String]
???
sarscov2_illumina_full.vadr_outputs
Array[File]
???
Generated using WDL AID (1.0.0)