4.24. demux_deplete¶
Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory, followed by QC metrics, depletion, and SRA submission prep.
4.24.1. Inputs¶
4.24.1.1. Required inputs¶
demux_deplete.flowcell_tgz
File — Default: None
Illumina BCL directory compressed as tarball. Must contain RunInfo.xml, SampleSheet.csv, RTAComplete.txt, and Data/Intensities/BaseCalls/*
demux_deplete.samplesheets
Array[File]+ — Default: None
Custom formatted 'extended' format tsv samplesheets that will override any SampleSheet.csv in the illumina BCL directory. Must supply one file per lane of the flowcell, and must provide them in lane order. Required tsv column headings are: sample, library_id_per_sample, barcode_1, barcode_2 (if paired reads, omit if single-end), library_strategy, library_source, library_selection, design_description. 'sample' must correspond to a biological sample. 'sample' x 'library_id_per_sample' must be unique within a samplesheet and correspond to independent libraries from the same original sample. barcode_1 and barcode_2 must correspond to the actual index sequence. Remaining columns must follow strict ontology: see 3rd tab of https://www.ncbi.nlm.nih.gov/core/assets/sra/files/SRA_metadata_acc_example.xlsx for controlled vocabulary and term definitions.
demux_deplete.spikein_db
File — Default: None
Synthetic sequences (e.g. ERCC, SDSI) that are used to track potential contamination within sequencing plate processing.
4.24.1.2. Advanced inputs¶
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demux_deplete.biosample_map
File? — Default: None
A two-column tsv that contains at least the following columns: sample_name, accession. sample_name refers to the external sample id, accession is the NCBI BioSample accession number (SAMNxxx). If this file is omitted, SRA submission prep will be skipped.
demux_deplete.bmtaggerDbs
Array[File]? — Default: None
Tool that can discriminate between human and bacterial reads and other reads by using short fragments. Databases must be provided to onset depletion.Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.
demux_deplete.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.
demux_deplete.read_structure
String? — Default: None
Details how the bases should be organized into logical reads.
demux_deplete.sample_rename_map
File? — Default: None
If 'samples' need to be renamed, provide a two-column tsv that contains at least the following columns: internal_id, external_id. All samples will be renamed prior to analysis. Any samples described in the samplesheets that are not present in sample_rename_map will be unaltered. If this is omitted, no samples will be renamed.
demux_deplete.sort_reads
Boolean — Default: true
Output bam files will be sorted by read name.
4.24.1.3. Other inputs¶
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demux_deplete.blastDbs
Array[File]? — Default: None
???
demux_deplete.bwaDbs
Array[File]? — Default: None
???
demux_deplete.default_filename_keys
Array[String] — Default: ["spike_in", "batch_lib"]
???
demux_deplete.default_sample_keys
Array[String] — Default: ["amplicon_set", "control", "batch_lib", "viral_ct"]
???
demux_deplete.deplete.clear_tags
Boolean? — Default: false
???
demux_deplete.deplete.cpu
Int? — Default: 8
???
demux_deplete.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???
demux_deplete.deplete.machine_mem_gb
Int? — Default: None
???
demux_deplete.deplete.query_chunk_size
Int? — Default: None
???
demux_deplete.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???
demux_deplete.illumina_demux.disk_size
Int — Default: 2625
???
demux_deplete.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
demux_deplete.illumina_demux.flowcell
String? — Default: None
???
demux_deplete.illumina_demux.machine_mem_gb
Int? — Default: None
???
demux_deplete.illumina_demux.maxMismatches
Int? — Default: 0
???
demux_deplete.illumina_demux.maxNoCalls
Int? — Default: None
???
demux_deplete.illumina_demux.maxRecordsInRam
Int? — Default: None
???
demux_deplete.illumina_demux.minimumBaseQuality
Int? — Default: 10
???
demux_deplete.illumina_demux.minimumQuality
Int? — Default: None
???
demux_deplete.illumina_demux.minMismatchDelta
Int? — Default: None
???
demux_deplete.illumina_demux.runStartDate
String? — Default: None
???
demux_deplete.illumina_demux.sequencingCenter
String? — Default: None
???
demux_deplete.illumina_demux.threads
Int? — Default: None
???
demux_deplete.instrument_model_user_specified
String? — Default: None
???
demux_deplete.min_reads_per_bam
Int — Default: 100
???
demux_deplete.multiqc_cleaned.comment
String? — Default: None
???
demux_deplete.multiqc_cleaned.config
File? — Default: None
???
demux_deplete.multiqc_cleaned.config_yaml
String? — Default: None
???
demux_deplete.multiqc_cleaned.data_dir
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???
demux_deplete.multiqc_cleaned.exclude_modules
Array[String]? — Default: None
???
demux_deplete.multiqc_cleaned.export
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.flat
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.force
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.full_names
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.ignore_analysis_files
String? — Default: None
???
demux_deplete.multiqc_cleaned.ignore_sample_names
String? — Default: None
???
demux_deplete.multiqc_cleaned.interactive
Boolean — Default: true
???
demux_deplete.multiqc_cleaned.lint
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.megaQC_upload
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.module_to_use
Array[String]? — Default: None
???
demux_deplete.multiqc_cleaned.no_data_dir
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.out_dir
String — Default: "./multiqc-output"
???
demux_deplete.multiqc_cleaned.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv
demux_deplete.multiqc_cleaned.pdf
Boolean — Default: false
???
demux_deplete.multiqc_cleaned.sample_names
File? — Default: None
???
demux_deplete.multiqc_cleaned.tag
String? — Default: None
???
demux_deplete.multiqc_cleaned.template
String? — Default: None
???
demux_deplete.multiqc_cleaned.title
String? — Default: None
???
demux_deplete.multiqc_cleaned.zip_data_dir
Boolean — Default: false
???
demux_deplete.multiqc_raw.comment
String? — Default: None
???
demux_deplete.multiqc_raw.config
File? — Default: None
???
demux_deplete.multiqc_raw.config_yaml
String? — Default: None
???
demux_deplete.multiqc_raw.data_dir
Boolean — Default: false
???
demux_deplete.multiqc_raw.docker
String — Default: "quay.io/biocontainers/multiqc:1.8--py_2"
???
demux_deplete.multiqc_raw.exclude_modules
Array[String]? — Default: None
???
demux_deplete.multiqc_raw.export
Boolean — Default: false
???
demux_deplete.multiqc_raw.flat
Boolean — Default: false
???
demux_deplete.multiqc_raw.force
Boolean — Default: false
???
demux_deplete.multiqc_raw.full_names
Boolean — Default: false
???
demux_deplete.multiqc_raw.ignore_analysis_files
String? — Default: None
???
demux_deplete.multiqc_raw.ignore_sample_names
String? — Default: None
???
demux_deplete.multiqc_raw.interactive
Boolean — Default: true
???
demux_deplete.multiqc_raw.lint
Boolean — Default: false
???
demux_deplete.multiqc_raw.megaQC_upload
Boolean — Default: false
???
demux_deplete.multiqc_raw.module_to_use
Array[String]? — Default: None
???
demux_deplete.multiqc_raw.no_data_dir
Boolean — Default: false
???
demux_deplete.multiqc_raw.out_dir
String — Default: "./multiqc-output"
???
demux_deplete.multiqc_raw.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv
demux_deplete.multiqc_raw.pdf
Boolean — Default: false
???
demux_deplete.multiqc_raw.sample_names
File? — Default: None
???
demux_deplete.multiqc_raw.tag
String? — Default: None
???
demux_deplete.multiqc_raw.template
String? — Default: None
???
demux_deplete.multiqc_raw.title
String? — Default: None
???
demux_deplete.multiqc_raw.zip_data_dir
Boolean — Default: false
???
demux_deplete.samplesheet_rename_ids.new_id_col
String — Default: 'external_id'
???
demux_deplete.samplesheet_rename_ids.old_id_col
String — Default: 'internal_id'
???
demux_deplete.spike_summary.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
demux_deplete.spike_summary.output_prefix
String — Default: "count_summary"
???
demux_deplete.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
demux_deplete.spikein.machine_mem_gb
Int? — Default: None
???
demux_deplete.spikein.topNHits
Int — Default: 3
???
demux_deplete.sra_meta_prep.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
demux_deplete.sra_title
String? — Default: None
???
4.24.2. Outputs¶
demux_deplete.cleaned_bam_uris
File?
A text file containing a string-serialized version of each File in cleaned_reads_unaligned_bams on a separate line.
demux_deplete.cleaned_bams_tiny
Array[File]
cleaned BAM files that contain less than min_reads_per_bam will be included here and omitted from cleaned_reads_unaligned_bams and cleaned_bam_uris
demux_deplete.cleaned_reads_unaligned_bams
Array[File]
Unaligned reads without human reads or PCR duplicates in BAM format. This will not include any bams that contain less than min_reads_per_bam reads.
demux_deplete.demux_commonBarcodes
Array[File]
a TSV report of all barcode counts, in descending order.
demux_deplete.demux_metrics
Array[File]
Output ExtractIlluminaBarcodes metrics file.
demux_deplete.demux_outlierBarcodes
Array[File]
???
demux_deplete.demux_viral_core_version
String
???
demux_deplete.instrument_model_inferred
String
???
demux_deplete.meta_by_filename
Map[String,Map[String,String]]
???
demux_deplete.meta_by_filename_json
File
???
demux_deplete.meta_by_sample
Map[String,Map[String,String]]
???
demux_deplete.meta_by_sample_json
File
???
demux_deplete.multiqc_report_cleaned
File
Aggregate results from QC analyses across many samples into a single report.
demux_deplete.multiqc_report_raw
File
???
demux_deplete.raw_reads_unaligned_bams
Array[File]
Unaligned reads in BAM format.
demux_deplete.read_counts_depleted
Array[Int]
???
demux_deplete.read_counts_raw
Array[Int]
A list of the read counts of each file in raw_reads_unaligned_bams
demux_deplete.run_date
String
???
demux_deplete.run_id
String
???
demux_deplete.run_info
Map[String,String]
???
demux_deplete.run_info_json
File
???
demux_deplete.spikein_counts
File
???
demux_deplete.sra_metadata
File?
???
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