4.67. 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.
4.67.1. Inputs¶
4.67.1.1. 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.gisaid_meta_prep.submitting_lab_name
String — Default: None
???
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####).
4.67.1.2. Advanced inputs¶
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sarscov2_sra_to_genbank.assemble_refbased.call_consensus.mark_duplicates
Boolean — Default: false
Instead of removing duplicates, simply marks them.
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)
4.67.1.3. Other inputs¶
Show/Hide
sarscov2_sra_to_genbank.assemble_refbased.align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
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_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_sra_to_genbank.assemble_refbased.align_to_self.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
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.align_to_self_options
Map[String,String] — Default: {"novoalign": "-r Random -l 40 -g 40 -x 20 -t 100", "bwa": "", "minimap2": ""}
???
sarscov2_sra_to_genbank.assemble_refbased.alignment_metrics.amplicon_set
String? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.alignment_metrics.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_sra_to_genbank.assemble_refbased.alignment_metrics.machine_mem_gb
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.alignment_metrics.max_amp_len
Int? — Default: 5000
???
sarscov2_sra_to_genbank.assemble_refbased.alignment_metrics.max_amplicons
Int? — Default: 500
???
sarscov2_sra_to_genbank.assemble_refbased.call_consensus.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.33.0"
???
sarscov2_sra_to_genbank.assemble_refbased.call_consensus.machine_mem_gb
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.isnvs_ref.docker
String — Default: "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
???
sarscov2_sra_to_genbank.assemble_refbased.isnvs_ref.out_basename
String — Default: basename(aligned_bam,'.bam')
???
sarscov2_sra_to_genbank.assemble_refbased.isnvs_self.docker
String — Default: "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
???
sarscov2_sra_to_genbank.assemble_refbased.isnvs_self.out_basename
String — Default: basename(aligned_bam,'.bam')
???
sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.bam_basename
String — Default: basename(aligned_bam,".bam")
???
sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.disk_size
Int — Default: 375
???
sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.docker
String — Default: "andersenlabapps/ivar:1.3.1"
???
sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.machine_mem_gb
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.ivar_trim.primer_offset
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.major_cutoff
Float — Default: 0.75
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.merge_align_to_ref.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
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:2.1.33"
???
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
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.base_q_threshold
Int? — Default: None
???
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:2.1.33"
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.mapping_q_threshold
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.max_coverage_depth
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.plot_height_pixels
Int? — Default: 850
???
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.plot_pixels_per_inch
Int? — Default: 100
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.plot_width_pixels
Int? — Default: 1100
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.plotXLimits
String? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.plotYLimits
String? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.read_length_threshold
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_ref_coverage.skip_mark_dupes
Boolean — Default: false
???
sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.base_q_threshold
Int? — Default: None
???
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:2.1.33"
???
sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.mapping_q_threshold
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.max_coverage_depth
Int? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.plot_height_pixels
Int? — Default: 850
???
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.plot_pixels_per_inch
Int? — Default: 100
???
sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.plot_width_pixels
Int? — Default: 1100
???
sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.plotXLimits
String? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.plotYLimits
String? — Default: None
???
sarscov2_sra_to_genbank.assemble_refbased.plot_self_coverage.read_length_threshold
Int? — Default: None
???
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:2.1.33"
???
sarscov2_sra_to_genbank.assembly_meta_tsv.cpus
Int — Default: 4
???
sarscov2_sra_to_genbank.biosample_to_genbank.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"
???
sarscov2_sra_to_genbank.biosample_to_genbank.s_dropout_note
Boolean — Default: true
???
sarscov2_sra_to_genbank.fastqc.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_sra_to_genbank.Fetch_SRA_to_BAM.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???
sarscov2_sra_to_genbank.Fetch_SRA_to_BAM.machine_mem_gb
Int? — Default: None
???
sarscov2_sra_to_genbank.gisaid_meta_prep.address_map
String — Default: '{}'
???
sarscov2_sra_to_genbank.gisaid_meta_prep.authors_map
String — Default: '{}'
???
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.username
String? — Default: None
???
sarscov2_sra_to_genbank.max_vadr_alerts
Int — Default: 0
???
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:2.1.33"
???
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.disk_size
Int — Default: 50
???
sarscov2_sra_to_genbank.sarscov2_lineages.nextclade_one_sample.docker
String — Default: "nextstrain/nextclade:2.12.0"
???
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.nextclade_one_sample.virus_properties
File? — Default: None
???
sarscov2_sra_to_genbank.sarscov2_lineages.pangolin_one_sample.analysis_mode
String? — Default: None
???
sarscov2_sra_to_genbank.sarscov2_lineages.pangolin_one_sample.docker
String — Default: "quay.io/staphb/pangolin:4.3.1-pdata-1.22"
???
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.sarscov2_lineages.pangolin_one_sample.update_dbs_now
Boolean — Default: false
???
sarscov2_sra_to_genbank.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
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:2.1.33"
???
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:2.1.33"
???
sarscov2_sra_to_genbank.submit_genomes.cpus
Int — Default: 4
???
sarscov2_sra_to_genbank.vadr.cpus
Int — Default: 2
???
sarscov2_sra_to_genbank.vadr.docker
String — Default: "quay.io/staphb/vadr:1.5.1"
???
sarscov2_sra_to_genbank.vadr.maxlen
Int — Default: 30000
???
sarscov2_sra_to_genbank.vadr.mem_size
Int — Default: 4
???
sarscov2_sra_to_genbank.vadr.minlen
Int — Default: 50
???
sarscov2_sra_to_genbank.vadr.vadr_opts
String — Default: "--glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn"
???
4.67.2. Outputs¶
sarscov2_sra_to_genbank.assembled_ids
Array[String]
???
sarscov2_sra_to_genbank.assemblies_fasta
Array[File]
???
sarscov2_sra_to_genbank.assembly_stats_tsv
File
???
sarscov2_sra_to_genbank.biosample_attributes
File
???
sarscov2_sra_to_genbank.cleaned_reads_unaligned_bams
Array[File]
???
sarscov2_sra_to_genbank.failed_annotation_ids
Array[String]
???
sarscov2_sra_to_genbank.failed_assembly_ids
Array[String]
???
sarscov2_sra_to_genbank.genbank_source_table
File
???
sarscov2_sra_to_genbank.gisaid_fasta
File
???
sarscov2_sra_to_genbank.gisaid_meta_csv
File
???
sarscov2_sra_to_genbank.multiqc_report_raw
File
???
sarscov2_sra_to_genbank.num_assembled
Int
???
sarscov2_sra_to_genbank.num_failed_annotation
Int
???
sarscov2_sra_to_genbank.num_failed_assembly
Int
???
sarscov2_sra_to_genbank.num_read_files
Int
???
sarscov2_sra_to_genbank.num_samples
Int
???
sarscov2_sra_to_genbank.num_submittable
Int
???
sarscov2_sra_to_genbank.passing_assemblies_fasta
Array[File]
???
sarscov2_sra_to_genbank.primer_trimmed_read_count
Array[Int]
???
sarscov2_sra_to_genbank.primer_trimmed_read_percent
Array[Float]
???
sarscov2_sra_to_genbank.raw_reads_unaligned_bams
Array[File]
???
sarscov2_sra_to_genbank.read_counts_depleted
Array[Int]
???
sarscov2_sra_to_genbank.read_counts_raw
Array[Int]
???
sarscov2_sra_to_genbank.spikein_counts
File
???
sarscov2_sra_to_genbank.submission_xml
File
???
sarscov2_sra_to_genbank.submission_zip
File
???
sarscov2_sra_to_genbank.submit_ready
File
???
sarscov2_sra_to_genbank.submittable_assemblies_fasta
Array[File]
???
sarscov2_sra_to_genbank.submittable_ids
Array[String]
???
sarscov2_sra_to_genbank.vadr_outputs
Array[File]
???
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