Description

Demultiplex Illumina BCL data using bcl-convert or bcl2fastq

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘string’, lane: int ]

samplesheet (file)

CSV file containing information about samples to be demultiplexed in Illumina SampleSheet format

flowcell (file)

Directory or tar archive containing Illumina BCL data, sequencer output directory

demultiplexer (string)

Which demultiplexer to use, bcl2fastq or bclconvert

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’ ]

fastq (file)

Demultiplexed fastq files

*.fastq.gz

reports (file)

Demultiplexing reports

Reports/*

interop (file)

InterOp files

InterOp/*

stats (file)

Demultiplexing statistics (bcl2fastq only)

Stats/*

versions (file)

File containing software versions

versions.yml
included in
demultiplex
author
Github user matthdsm
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