4.29. demux_only

Picard-based demultiplexing and basecalling from a tarball of a raw BCL directory.

4.29.1. Inputs

4.29.1.1. Required inputs

demux_only.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_only.illumina_demux.samplesheet
File? — Default: None
TSV or CSV file with sample names, library IDs, and the barcode or barcodes (indices) associated with each sample, in addition to other per-sample attributes.

4.29.1.2. Advanced inputs

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demux_only.illumina_demux.barcode_columns_to_rev_comp
Array[String]? — Default: None
Columns in the sample sheet to reverse-complement. Only used if 'rev_comp_barcodes_before_demux' is true. Defaults to 'barcode_2'.

demux_only.illumina_demux.rev_comp_barcodes_before_demux
Boolean — Default: false
Reverse-complement the barcode(s) before demultiplexing. By default, this action applies to values in the 'barcode_2' column unless overridden by 'barcode_columns_to_rev_comp'.

demux_only.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.

4.29.1.3. Other inputs

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demux_only.illumina_demux.disk_size
Int — Default: 2625
???

demux_only.illumina_demux.docker
String — Default: "quay.io/broadinstitute/viral-core:2.5.16"
???

demux_only.illumina_demux.emit_unmatched_reads_bam
Boolean — Default: false
???

demux_only.illumina_demux.firstTile
Int? — Default: None
???

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

demux_only.illumina_demux.inner_barcode_predemux_trim_r1_3prime
Int — Default: 18
???

demux_only.illumina_demux.inner_barcode_predemux_trim_r2_3prime
Int — Default: 18
???

demux_only.illumina_demux.inner_barcode_predemux_trim_r2_5prime
Int — Default: 18
???

demux_only.illumina_demux.inner_barcode_trim_r1_right_of_barcode
Int — Default: 10
???

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

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

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

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

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

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

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

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

demux_only.illumina_demux.numberOfNegativeControls
Int? — Default: None
???

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

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

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

demux_only.illumina_demux.sort_reads
Boolean — Default: true
???

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

demux_only.illumina_demux.tileLimit
Int? — Default: None
???

demux_only.instrument_model_user_specified
String? — Default: None
???

demux_only.multiqc.comment
String? — Default: None
???

demux_only.multiqc.config
File? — Default: None
???

demux_only.multiqc.config_yaml
String? — Default: None
???

demux_only.multiqc.docker
String — Default: "ghcr.io/broadinstitute/read-qc-tools:1.0.1"
???

demux_only.multiqc.full_names
Boolean — Default: false
???

demux_only.multiqc.interactive
Boolean — Default: true
???

demux_only.multiqc.title
String? — Default: None
???

4.29.2. Outputs

demux_only.demux_commonBarcodes
File
???

demux_only.demux_metrics
File
???

demux_only.demux_outlierBarcodes
File
???

demux_only.demux_viral_core_version
String
???

demux_only.fastqcs
Array[File]
???

demux_only.instrument_model_inferred
String
???

demux_only.meta_by_filename
Map[String,Map[String,String]]
???

demux_only.meta_by_filename_json
File
???

demux_only.meta_by_sample
Map[String,Map[String,String]]
???

demux_only.meta_by_sample_json
File
???

demux_only.multiqc_report_raw
File
???

demux_only.raw_reads_unaligned_bams
Array[File]
???

demux_only.run_date
String
???

demux_only.run_id
String
???

demux_only.run_info
Map[String,String]
???

demux_only.run_info_json
File
???

demux_only.run_lane_count
String
???

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