Demultiplex Illumina BCL files
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
samplesheet:file
Input samplesheet
*.{csv}
run_dir:file
Input run directory containing RunInfo.xml and BCL data Could be a directory or a tar of the directory
fastq
meta:file
Demultiplexed sample FASTQ files
**_S*_L00?_R?_00?.fastq.gz
output/**_S[1-9]*_R?_00?.fastq.gz:file
fastq_idx
Optional demultiplexed index FASTQ files
**_S*_L00?_I?_00?.fastq.gz
output/**_S[1-9]*_I?_00?.fastq.gz:file
undetermined
Optional undetermined sample FASTQ files
Undetermined_S0_L00?_R?_00?.fastq.gz
output/**Undetermined_S0*_R?_00?.fastq.gz:file
undetermined_idx
Optional undetermined index FASTQ files
Undetermined_S0_L00?_I?_00?.fastq.gz
output/**Undetermined_S0*_I?_00?.fastq.gz:file
reports
Demultiplexing Reports
Reports/*
output/Reports:file
stats
Statistics files
Stats/*
output/Stats:file
interop
Interop files
*.{bin}
InterOp/*.bin:file
versions
versions.yml:file
File containing software versions
versions.yml
