bcl_demultiplex
Demultiplex Illumina BCL data using bcl-convert or bcl2fastq
Input
Channel containing the Illumina SampleSheet CSV describing the samples to be
demultiplexed, together with the directory or tar archive holding the Illumina
BCL data (the sequencer output directory). The meta map carries the flowcell
identifier and lane, e.g. [ id:‘string’, lane: int ].
Structure: [ val(meta), path(samplesheet), path(flowcell) ]
Output
Demultiplexed FASTQ files, with read group information added to the meta map.
Samples whose FASTQ files are empty are routed to empty_fastq instead.
Structure: [ val(meta), [ path(fastq) ] ]
*.fastq.gzDemultiplexed FASTQ files that contain no reads, separated out so that
downstream processes do not have to handle them.
Structure: [ val(meta), [ path(fastq) ] ]
*.fastq.gzFASTQ files holding the reads that could not be assigned to any sample.
Structure: [ val(meta), [ path(fastq) ] ]
Undetermined_S0*_R?_00?.fastq.gzMultiQC report summarising the sequencing analysis viewer (SAV) metrics for
the flowcell.
Structure: [ val(meta), path(html) ]
*.htmlincluded in
included modules and subworkflows
maintainer
