4.22. demux_plus

Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory, followed by basic metagenomics and QC metrics. Intended for automatic triggering post upload on DNAnexus.

4.22.1. Inputs

4.22.1.1. Required inputs

demux_plus.illumina_demux.flowcell_tgz
File — Default: None
???

demux_plus.krakenuniq.krakenuniq_db_tar_lz4
File — Default: None
Pre-built Kraken database tarball.

demux_plus.krakenuniq.krona_taxonomy_db_tgz
File — Default: None
Krona taxonomy database containing a single file: taxonomy.tab, or possibly just a compressed taxonomy.tab

demux_plus.spikein_db
File — Default: None
???

demux_plus.trim_clip_db
File — Default: None
???

4.22.1.2. Other inputs

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demux_plus.blastDbs
Array[File]? — Default: None
???

demux_plus.bmtaggerDbs
Array[File]? — Default: None
???

demux_plus.bwaDbs
Array[File]? — Default: None
???

demux_plus.deplete.clear_tags
Boolean? — Default: false
???

demux_plus.deplete.cpu
Int? — Default: 8
???

demux_plus.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.10.0"
???

demux_plus.deplete.machine_mem_gb
Int? — Default: None
???

demux_plus.deplete.query_chunk_size
Int? — Default: None
???

demux_plus.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

demux_plus.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

demux_plus.illumina_demux.flowcell
String? — Default: None
???

demux_plus.illumina_demux.forceGC
Boolean? — Default: true
???

demux_plus.illumina_demux.lane
Int? — Default: 1
???

demux_plus.illumina_demux.machine_mem_gb
Int? — Default: None
???

demux_plus.illumina_demux.maxMismatches
Int? — Default: 0
???

demux_plus.illumina_demux.maxNoCalls
Int? — Default: None
???

demux_plus.illumina_demux.maxReadsInRamPerTile
Int? — Default: None
???

demux_plus.illumina_demux.maxRecordsInRam
Int? — Default: None
???

demux_plus.illumina_demux.minimumBaseQuality
Int? — Default: 10
???

demux_plus.illumina_demux.minimumQuality
Int? — Default: None
???

demux_plus.illumina_demux.minMismatchDelta
Int? — Default: None
???

demux_plus.illumina_demux.readStructure
String? — Default: None
???

demux_plus.illumina_demux.runinfo
File? — Default: None
???

demux_plus.illumina_demux.runStartDate
String? — Default: None
???

demux_plus.illumina_demux.samplesheet
File? — Default: None
???

demux_plus.illumina_demux.sequencingCenter
String? — Default: None
???

demux_plus.illumina_demux.threads
Int? — Default: None
???

demux_plus.krakenuniq.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.10.0"
???

demux_plus.krakenuniq.machine_mem_gb
Int? — Default: None
???

demux_plus.metag_summary_report.aggregate_taxlevel_focus
String — Default: "species"
species,genus,family,order,class,phylum,kingdom,superkingdom

demux_plus.metag_summary_report.aggregate_taxon_heading_space_separated
String — Default: "Viruses"
The taxonomic heading to analyze. More than one can be specified.

demux_plus.metag_summary_report.aggregate_top_N_hits
Int — Default: 5
only include the top N hits from a given sample in the aggregate report

demux_plus.metag_summary_report.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.10.0"
???

demux_plus.multiqc_cleaned.comment
String? — Default: None
???

demux_plus.multiqc_cleaned.config
File? — Default: None
???

demux_plus.multiqc_cleaned.config_yaml
String? — Default: None
???

demux_plus.multiqc_cleaned.data_dir
Boolean — Default: false
???

demux_plus.multiqc_cleaned.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

demux_plus.multiqc_cleaned.exclude_modules
Array[String]? — Default: None
???

demux_plus.multiqc_cleaned.export
Boolean — Default: false
???

demux_plus.multiqc_cleaned.flat
Boolean — Default: false
???

demux_plus.multiqc_cleaned.force
Boolean — Default: false
???

demux_plus.multiqc_cleaned.full_names
Boolean — Default: false
???

demux_plus.multiqc_cleaned.ignore_analysis_files
String? — Default: None
???

demux_plus.multiqc_cleaned.ignore_sample_names
String? — Default: None
???

demux_plus.multiqc_cleaned.interactive
Boolean — Default: true
???

demux_plus.multiqc_cleaned.lint
Boolean — Default: false
???

demux_plus.multiqc_cleaned.megaQC_upload
Boolean — Default: false
???

demux_plus.multiqc_cleaned.module_to_use
Array[String]? — Default: None
???

demux_plus.multiqc_cleaned.no_data_dir
Boolean — Default: false
???

demux_plus.multiqc_cleaned.out_dir
String — Default: "./multiqc-output"
???

demux_plus.multiqc_cleaned.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_plus.multiqc_cleaned.pdf
Boolean — Default: false
???

demux_plus.multiqc_cleaned.sample_names
File? — Default: None
???

demux_plus.multiqc_cleaned.tag
String? — Default: None
???

demux_plus.multiqc_cleaned.template
String? — Default: None
???

demux_plus.multiqc_cleaned.title
String? — Default: None
???

demux_plus.multiqc_cleaned.zip_data_dir
Boolean — Default: false
???

demux_plus.multiqc_raw.comment
String? — Default: None
???

demux_plus.multiqc_raw.config
File? — Default: None
???

demux_plus.multiqc_raw.config_yaml
String? — Default: None
???

demux_plus.multiqc_raw.data_dir
Boolean — Default: false
???

demux_plus.multiqc_raw.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???

demux_plus.multiqc_raw.exclude_modules
Array[String]? — Default: None
???

demux_plus.multiqc_raw.export
Boolean — Default: false
???

demux_plus.multiqc_raw.flat
Boolean — Default: false
???

demux_plus.multiqc_raw.force
Boolean — Default: false
???

demux_plus.multiqc_raw.full_names
Boolean — Default: false
???

demux_plus.multiqc_raw.ignore_analysis_files
String? — Default: None
???

demux_plus.multiqc_raw.ignore_sample_names
String? — Default: None
???

demux_plus.multiqc_raw.interactive
Boolean — Default: true
???

demux_plus.multiqc_raw.lint
Boolean — Default: false
???

demux_plus.multiqc_raw.megaQC_upload
Boolean — Default: false
???

demux_plus.multiqc_raw.module_to_use
Array[String]? — Default: None
???

demux_plus.multiqc_raw.no_data_dir
Boolean — Default: false
???

demux_plus.multiqc_raw.out_dir
String — Default: "./multiqc-output"
???

demux_plus.multiqc_raw.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_plus.multiqc_raw.pdf
Boolean — Default: false
???

demux_plus.multiqc_raw.sample_names
File? — Default: None
???

demux_plus.multiqc_raw.tag
String? — Default: None
???

demux_plus.multiqc_raw.template
String? — Default: None
???

demux_plus.multiqc_raw.title
String? — Default: None
???

demux_plus.multiqc_raw.zip_data_dir
Boolean — Default: false
???

demux_plus.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.10.0"
???

demux_plus.spades.machine_mem_gb
Int? — Default: None
???

demux_plus.spades.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".taxfilt")
???

demux_plus.spades.spades_min_contig_len
Int? — Default: 0
???

demux_plus.spades.spades_n_reads
Int? — Default: 10000000
???

demux_plus.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

demux_plus.spike_summary.output_prefix
String — Default: "count_summary"
???

demux_plus.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.10"
???

demux_plus.spikein.machine_mem_gb
Int? — Default: None
???

demux_plus.spikein.topNHits
Int — Default: 3
???

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