4.19. classify_multi¶
Runs raw reads through taxonomic classification (Kraken2), human read depletion (based on Kraken2), de novo assembly (SPAdes), and FASTQC/multiQC of reads.
4.19.1. Inputs¶
4.19.1.1. 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.spades.spades_n_reads
Int — Default: 10000000
Subsample reads threshold prior to assembly. Default set to 10000000
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
4.19.1.2. Other inputs¶
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classify_multi.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???
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:2.1.33"
???
classify_multi.fastqc_raw.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
classify_multi.filter_acellular.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???
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:2.1.33.0"
???
classify_multi.kraken2.machine_mem_gb
Int — Default: 72
???
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:2.1.33.0"
???
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:2.1.33.0"
???
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:2.1.33"
???
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:2.1.33.0"
???
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: None
Minimum length of output contig.
classify_multi.spades.spades_options
String? — Default: None
Display additional options to pass the SPAdes assembler.
classify_multi.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
classify_multi.spike_summary.output_prefix
String — Default: "count_summary"
???
classify_multi.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
classify_multi.spikein.machine_mem_gb
Int? — Default: None
???
classify_multi.spikein.topNHits
Int — Default: 3
???
4.19.2. Outputs¶
classify_multi.cleaned_reads_unaligned_bams
Array[File]
???
classify_multi.contigs_fastas
Array[File]
???
classify_multi.deduplicated_reads_unaligned
Array[File]
???
classify_multi.deplete_viral_classify_version
String
???
classify_multi.kraken2_krona_by_sample
Array[File]
???
classify_multi.kraken2_merged_krona
File
???
classify_multi.kraken2_summary
File
???
classify_multi.kraken2_summary_reports
Array[File]
???
classify_multi.kraken2_viral_classify_version
String
???
classify_multi.multiqc_report_cleaned
File
???
classify_multi.multiqc_report_dedup
File
???
classify_multi.multiqc_report_raw
File
???
classify_multi.read_counts_dedup
Array[Int]
???
classify_multi.read_counts_depleted
Array[Int]
???
classify_multi.read_counts_prespades_subsample
Array[Int]
???
classify_multi.read_counts_raw
Array[Int]
???
classify_multi.spades_viral_assemble_version
String
???
classify_multi.spikein_counts
File
???
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