4.22. classify_single¶
Runs raw reads through taxonomic classification (Kraken2), human read depletion (based on Kraken2), de novo assembly (SPAdes), and FASTQC/multiQC of reads.
4.22.1. Inputs¶
4.22.1.1. Required inputs¶
classify_single.kraken2_db_tgz
File — Default: None
Pre-built Kraken database tarball containing three files: hash.k2d, opts.k2d, and taxo.k2d.
classify_single.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_single.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_single.reads_bams
Array[File]+ — Default: None
Reads to classify. May be unmapped or mapped or both, paired-end or single-end. Multiple input files will be merged first.
classify_single.spades.spades_n_reads
Int — Default: 10000000
Subsample reads threshold prior to assembly. Default set to 10000000
classify_single.spikein_db
File — Default: None
ERCC spike-in sequences
classify_single.trim_clip_db
File — Default: None
Adapter sequences to remove via trimmomatic prior to SPAdes assembly
4.22.1.2. Other inputs¶
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classify_single.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.2.4.2"
???
classify_single.deplete.machine_mem_gb
Int — Default: 26
???
classify_single.deplete.minimum_hit_groups
Int? — Default: None
???
classify_single.deplete.taxonomic_ids
Array[Int]? — Default: None
???
classify_single.deplete.withoutChildren
Boolean — Default: false
???
classify_single.fastqc_cleaned.docker
String — Default: "quay.io/broadinstitute/viral-core:2.3.6"
???
classify_single.filter_acellular.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.2.4.2"
???
classify_single.filter_acellular.machine_mem_gb
Int — Default: 26
???
classify_single.filter_acellular.minimum_hit_groups
Int? — Default: None
???
classify_single.filter_acellular.taxonomic_ids
Array[Int]? — Default: None
???
classify_single.filter_acellular.withoutChildren
Boolean — Default: false
???
classify_single.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_single.kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.2.4.2"
???
classify_single.kraken2.machine_mem_gb
Int — Default: 90
???
classify_single.kraken2.min_base_qual
Int? — Default: None
Minimum base quality used in classification
classify_single.merge_raw_reads.disk_size
Int — Default: 750
???
classify_single.merge_raw_reads.docker
String — Default: "quay.io/broadinstitute/viral-core:2.3.6"
???
classify_single.merge_raw_reads.machine_mem_gb
Int — Default: 4
???
classify_single.merge_raw_reads.out_basename
String — Default: basename(in_bams[0],".bam")
???
classify_single.merge_raw_reads.reheader_table
File? — Default: None
???
classify_single.merge_raw_reads.sample_name
String? — Default: None
???
classify_single.report_primary_kraken_taxa.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.2.4.2"
???
classify_single.report_primary_kraken_taxa.focal_taxon
String — Default: "Viruses"
???
classify_single.rmdup_ubam.docker
String — Default: "quay.io/broadinstitute/viral-core:2.3.6"
???
classify_single.rmdup_ubam.machine_mem_gb
Int — Default: 7
???
classify_single.rmdup_ubam.method
String — Default: "mvicuna"
mvicuna or cdhit
classify_single.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.3.6.1"
???
classify_single.spades.machine_mem_gb
Int? — Default: None
???
classify_single.spades.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".taxfilt")
???
classify_single.spades.spades_min_contig_len
Int? — Default: None
Minimum length of output contig.
classify_single.spades.spades_options
String? — Default: None
Display additional options to pass the SPAdes assembler.
classify_single.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.3.6"
???
classify_single.spikein.machine_mem_gb
Int? — Default: None
???
classify_single.spikein.topNHits
Int — Default: 3
???
classify_single.taxa_to_avoid_assembly
Array[String] — Default: ["Vertebrata", "other sequences", "Bacteria"]
???
classify_single.taxa_to_dehost
Array[String] — Default: ["Vertebrata"]
???
4.22.2. Outputs¶
classify_single.cleaned_fastqc
File
Output cleaned fastqc reports in HTML.
classify_single.cleaned_reads_unaligned_bam
File
???
classify_single.contigs_fasta
File
???
classify_single.deduplicated_reads_unaligned
File
Deduplication on unaligned reads in BAM format using mvicuna or cdhit.
classify_single.deplete_viral_classify_version
String
???
classify_single.kraken2_focal_taxon_name
String
???
classify_single.kraken2_focal_total_reads
Int
???
classify_single.kraken2_krona_plot
File
Visualize the results of the Kraken2 analysis with Krona, which disaplys taxonmic hierarchiral data in multi-layerd pie.
classify_single.kraken2_summary_report
File
Kraken report output file.
classify_single.kraken2_top_taxa_report
File
???
classify_single.kraken2_top_taxon_id
String
???
classify_single.kraken2_top_taxon_name
String
???
classify_single.kraken2_top_taxon_num_reads
Int
???
classify_single.kraken2_top_taxon_pct_of_focal
Float
???
classify_single.kraken2_top_taxon_rank
String
???
classify_single.kraken2_viral_classify_version
String
???
classify_single.raw_fastqc
File
Merged raw fastqc reads.
classify_single.read_counts_dedup
Int
???
classify_single.read_counts_depleted
Int
???
classify_single.read_counts_prespades_subsample
Int
???
classify_single.read_counts_raw
Int
???
classify_single.spades_viral_assemble_version
String
???
classify_single.spikein_pct_lesser_hits
String
???
classify_single.spikein_pct_of_total_reads
String
???
classify_single.spikein_report
File
???
classify_single.spikein_tophit
String
???
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