4.25. demux_metag¶
4.25.1. Inputs¶
4.25.1.1. Required inputs¶
demux_metag.illumina_demux.flowcell_tgz
File — Default: None
Illumina BCL directory compressed as tarball. Must contain RunInfo.xml (unless overridden by runinfo), SampleSheet.csv (unless overridden by samplesheet), RTAComplete.txt, and Data/Intensities/BaseCalls/*
demux_metag.illumina_demux.samplesheet
File? — Default: None
CSV file with the library chemistry, sample names and the index tag used for each sample, in addition to some other metrics describing the run.
demux_metag.kraken2_db_tgz
File — Default: None
???
demux_metag.krona_taxonomy_db_blast_tgz
File — Default: None
???
demux_metag.krona_taxonomy_db_kraken2_tgz
File — Default: None
???
demux_metag.spades.spades_n_reads
Int — Default: 10000000
Subsample reads threshold prior to assembly. Default set to 10000000
demux_metag.spikein_db
File — Default: None
???
demux_metag.trim_clip_db
File — Default: None
???
4.25.1.2. Advanced inputs¶
Show/Hide
demux_metag.illumina_demux.runinfo
File? — Default: None
if we are overriding the RunInfo file, use the path of the file provided. Otherwise the default will be RunInfo.xml.
4.25.1.3. Other inputs¶
Show/Hide
demux_metag.blastDbs
Array[File]? — Default: None
???
demux_metag.bmtaggerDbs
Array[File]? — Default: None
???
demux_metag.bwaDbs
Array[File]? — Default: None
???
demux_metag.deplete.clear_tags
Boolean? — Default: false
???
demux_metag.deplete.cpu
Int? — Default: 8
???
demux_metag.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???
demux_metag.deplete.machine_mem_gb
Int? — Default: None
???
demux_metag.deplete.query_chunk_size
Int? — Default: None
???
demux_metag.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???
demux_metag.illumina_demux.disk_size
Int — Default: 2625
???
demux_metag.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
demux_metag.illumina_demux.flowcell
String? — Default: None
???
demux_metag.illumina_demux.lane
Int — Default: 1
???
demux_metag.illumina_demux.machine_mem_gb
Int? — Default: None
???
demux_metag.illumina_demux.maxMismatches
Int? — Default: 0
???
demux_metag.illumina_demux.maxNoCalls
Int? — Default: None
???
demux_metag.illumina_demux.maxRecordsInRam
Int? — Default: None
???
demux_metag.illumina_demux.minimumBaseQuality
Int? — Default: 10
???
demux_metag.illumina_demux.minimumQuality
Int? — Default: None
???
demux_metag.illumina_demux.minMismatchDelta
Int? — Default: None
???
demux_metag.illumina_demux.readStructure
String? — Default: None
???
demux_metag.illumina_demux.runStartDate
String? — Default: None
???
demux_metag.illumina_demux.sequencingCenter
String? — Default: None
???
demux_metag.illumina_demux.sort_reads
Boolean — Default: true
???
demux_metag.illumina_demux.threads
Int? — Default: None
???
demux_metag.instrument_model_user_specified
String? — Default: None
???
demux_metag.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
demux_metag.kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???
demux_metag.kraken2.machine_mem_gb
Int — Default: 72
???
demux_metag.kraken2.min_base_qual
Int? — Default: None
Minimum base quality used in classification
demux_metag.krona_merge_kraken2.docker
String — Default: "biocontainers/krona:v2.7.1_cv1"
???
demux_metag.krona_merge_kraken2.machine_mem_gb
Int? — Default: None
???
demux_metag.metag_summary_report.aggregate_taxlevel_focus
String — Default: "species"
species,genus,family,order,class,phylum,kingdom,superkingdom
demux_metag.metag_summary_report.aggregate_taxon_heading_space_separated
String — Default: "Viruses"
The taxonomic heading to analyze. More than one can be specified.
demux_metag.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_metag.metag_summary_report.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???
demux_metag.multiqc_cleaned.comment
String? — Default: None
???
demux_metag.multiqc_cleaned.config
File? — Default: None
???
demux_metag.multiqc_cleaned.config_yaml
String? — Default: None
???
demux_metag.multiqc_cleaned.data_dir
Boolean — Default: false
???
demux_metag.multiqc_cleaned.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???
demux_metag.multiqc_cleaned.exclude_modules
Array[String]? — Default: None
???
demux_metag.multiqc_cleaned.export
Boolean — Default: false
???
demux_metag.multiqc_cleaned.flat
Boolean — Default: false
???
demux_metag.multiqc_cleaned.force
Boolean — Default: false
???
demux_metag.multiqc_cleaned.full_names
Boolean — Default: false
???
demux_metag.multiqc_cleaned.ignore_analysis_files
String? — Default: None
???
demux_metag.multiqc_cleaned.ignore_sample_names
String? — Default: None
???
demux_metag.multiqc_cleaned.interactive
Boolean — Default: true
???
demux_metag.multiqc_cleaned.lint
Boolean — Default: false
???
demux_metag.multiqc_cleaned.megaQC_upload
Boolean — Default: false
???
demux_metag.multiqc_cleaned.module_to_use
Array[String]? — Default: None
???
demux_metag.multiqc_cleaned.no_data_dir
Boolean — Default: false
???
demux_metag.multiqc_cleaned.out_dir
String — Default: "./multiqc-output"
???
demux_metag.multiqc_cleaned.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv
demux_metag.multiqc_cleaned.pdf
Boolean — Default: false
???
demux_metag.multiqc_cleaned.sample_names
File? — Default: None
???
demux_metag.multiqc_cleaned.tag
String? — Default: None
???
demux_metag.multiqc_cleaned.template
String? — Default: None
???
demux_metag.multiqc_cleaned.title
String? — Default: None
???
demux_metag.multiqc_cleaned.zip_data_dir
Boolean — Default: false
???
demux_metag.multiqc_dedup.comment
String? — Default: None
???
demux_metag.multiqc_dedup.config
File? — Default: None
???
demux_metag.multiqc_dedup.config_yaml
String? — Default: None
???
demux_metag.multiqc_dedup.data_dir
Boolean — Default: false
???
demux_metag.multiqc_dedup.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???
demux_metag.multiqc_dedup.exclude_modules
Array[String]? — Default: None
???
demux_metag.multiqc_dedup.export
Boolean — Default: false
???
demux_metag.multiqc_dedup.flat
Boolean — Default: false
???
demux_metag.multiqc_dedup.force
Boolean — Default: false
???
demux_metag.multiqc_dedup.full_names
Boolean — Default: false
???
demux_metag.multiqc_dedup.ignore_analysis_files
String? — Default: None
???
demux_metag.multiqc_dedup.ignore_sample_names
String? — Default: None
???
demux_metag.multiqc_dedup.interactive
Boolean — Default: true
???
demux_metag.multiqc_dedup.lint
Boolean — Default: false
???
demux_metag.multiqc_dedup.megaQC_upload
Boolean — Default: false
???
demux_metag.multiqc_dedup.module_to_use
Array[String]? — Default: None
???
demux_metag.multiqc_dedup.no_data_dir
Boolean — Default: false
???
demux_metag.multiqc_dedup.out_dir
String — Default: "./multiqc-output"
???
demux_metag.multiqc_dedup.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv
demux_metag.multiqc_dedup.pdf
Boolean — Default: false
???
demux_metag.multiqc_dedup.sample_names
File? — Default: None
???
demux_metag.multiqc_dedup.tag
String? — Default: None
???
demux_metag.multiqc_dedup.template
String? — Default: None
???
demux_metag.multiqc_dedup.title
String? — Default: None
???
demux_metag.multiqc_dedup.zip_data_dir
Boolean — Default: false
???
demux_metag.multiqc_raw.comment
String? — Default: None
???
demux_metag.multiqc_raw.config
File? — Default: None
???
demux_metag.multiqc_raw.config_yaml
String? — Default: None
???
demux_metag.multiqc_raw.data_dir
Boolean — Default: false
???
demux_metag.multiqc_raw.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???
demux_metag.multiqc_raw.exclude_modules
Array[String]? — Default: None
???
demux_metag.multiqc_raw.export
Boolean — Default: false
???
demux_metag.multiqc_raw.flat
Boolean — Default: false
???
demux_metag.multiqc_raw.force
Boolean — Default: false
???
demux_metag.multiqc_raw.full_names
Boolean — Default: false
???
demux_metag.multiqc_raw.ignore_analysis_files
String? — Default: None
???
demux_metag.multiqc_raw.ignore_sample_names
String? — Default: None
???
demux_metag.multiqc_raw.interactive
Boolean — Default: true
???
demux_metag.multiqc_raw.lint
Boolean — Default: false
???
demux_metag.multiqc_raw.megaQC_upload
Boolean — Default: false
???
demux_metag.multiqc_raw.module_to_use
Array[String]? — Default: None
???
demux_metag.multiqc_raw.no_data_dir
Boolean — Default: false
???
demux_metag.multiqc_raw.out_dir
String — Default: "./multiqc-output"
???
demux_metag.multiqc_raw.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv
demux_metag.multiqc_raw.pdf
Boolean — Default: false
???
demux_metag.multiqc_raw.sample_names
File? — Default: None
???
demux_metag.multiqc_raw.tag
String? — Default: None
???
demux_metag.multiqc_raw.template
String? — Default: None
???
demux_metag.multiqc_raw.title
String? — Default: None
???
demux_metag.multiqc_raw.zip_data_dir
Boolean — Default: false
???
demux_metag.rmdup_ubam.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
demux_metag.rmdup_ubam.machine_mem_gb
Int? — Default: None
???
demux_metag.rmdup_ubam.method
String — Default: "mvicuna"
mvicuna or cdhit
demux_metag.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.33.0"
???
demux_metag.spades.machine_mem_gb
Int? — Default: None
???
demux_metag.spades.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".taxfilt")
???
demux_metag.spades.spades_min_contig_len
Int? — Default: None
Minimum length of output contig.
demux_metag.spades.spades_options
String? — Default: None
Display additional options to pass the SPAdes assembler.
demux_metag.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
demux_metag.spike_summary.output_prefix
String — Default: "count_summary"
???
demux_metag.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
demux_metag.spikein.machine_mem_gb
Int? — Default: None
???
demux_metag.spikein.topNHits
Int — Default: 3
???
4.25.2. Outputs¶
demux_metag.cleaned_reads_unaligned_bams
Array[File]
???
demux_metag.contigs_fastas
Array[File]
???
demux_metag.deduplicated_reads_unaligned
Array[File]
???
demux_metag.demux_commonBarcodes
File
???
demux_metag.demux_metrics
File
???
demux_metag.demux_outlierBarcodes
File
???
demux_metag.demux_viral_core_version
String
???
demux_metag.deplete_viral_classify_version
String
???
demux_metag.instrument_model_inferred
String
???
demux_metag.kraken2_krona_by_sample
Array[File]
???
demux_metag.kraken2_merged_krona
File
???
demux_metag.kraken2_summary
File
???
demux_metag.kraken2_summary_reports
Array[File]
???
demux_metag.kraken2_viral_classify_version
String
???
demux_metag.multiqc_report_cleaned
File
???
demux_metag.multiqc_report_dedup
File
???
demux_metag.multiqc_report_raw
File
???
demux_metag.raw_reads_unaligned_bams
Array[File]
???
demux_metag.read_counts_dedup
Array[Int]
???
demux_metag.read_counts_depleted
Array[Int]
???
demux_metag.read_counts_prespades_subsample
Array[Int]
???
demux_metag.read_counts_raw
Array[Int]
???
demux_metag.spades_viral_assemble_version
String
???
demux_metag.spikein_counts
File
???
Generated using WDL AID (1.0.0)