4.21. demux_only

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

4.21.1. Inputs

4.21.1.1. Required inputs

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

4.21.1.2. Other inputs

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

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

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

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.maxReadsInRamPerTile
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.readStructure
String? — Default: None
???

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

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

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

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

demux_only.illumina_demux.threads
Int? — 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.data_dir
Boolean — Default: false
???

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

demux_only.MultiQC.exclude_modules
Array[String]? — Default: None
???

demux_only.MultiQC.export
Boolean — Default: false
???

demux_only.MultiQC.file_name
String? — Default: None
???

demux_only.MultiQC.flat
Boolean — Default: false
???

demux_only.MultiQC.force
Boolean — Default: false
???

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

demux_only.MultiQC.ignore_analysis_files
String? — Default: None
???

demux_only.MultiQC.ignore_sample_names
String? — Default: None
???

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

demux_only.MultiQC.lint
Boolean — Default: false
???

demux_only.MultiQC.megaQC_upload
Boolean — Default: false
???

demux_only.MultiQC.module_to_use
Array[String]? — Default: None
???

demux_only.MultiQC.no_data_dir
Boolean — Default: false
???

demux_only.MultiQC.out_dir
String — Default: "./multiqc-output"
???

demux_only.MultiQC.output_data_format
String? — Default: None
[tsv|yaml|json] default:tsv

demux_only.MultiQC.pdf
Boolean — Default: false
???

demux_only.MultiQC.sample_names
File? — Default: None
???

demux_only.MultiQC.tag
String? — Default: None
???

demux_only.MultiQC.template
String? — Default: None
???

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

demux_only.MultiQC.zip_data_dir
Boolean — Default: false
???

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