4.53. 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.
4.53.1. Inputs¶
4.53.1.1. 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.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####).
4.53.1.2. 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:1.3.1"
???
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:2.1.19.1"
???
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:2.1.19"
???
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.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:2.1.19"
???
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.docker
String — Default: "staphb/pangolin:2.3.2-pangolearn-2021-02-21"
???
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:1.1.3"
???
sarscov2_sra_to_genbank.vadr.vadr_opts
String — Default: "-s -r --nomisc --mkey NC_045512 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf,insertnn,deletinn"
???
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