Demultiplex Illumina BCL files
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
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
Groovy Map containing sample information
output/**_S[1-9]*_R?_00?.fastq.gz:file
Demultiplexed sample FASTQ files
**_S*_L00?_R?_00?.fastq.gz
fastq_idx
output/**_S[1-9]*_I?_00?.fastq.gz:file
Optional demultiplexed index FASTQ files
**_S*_L00?_I?_00?.fastq.gz
undetermined
output/**Undetermined_S0*_R?_00?.fastq.gz:file
Optional undetermined sample FASTQ files
Undetermined_S0_L00?_R?_00?.fastq.gz
undetermined_idx
output/**Undetermined_S0*_I?_00?.fastq.gz:file
Optional undetermined index FASTQ files
Undetermined_S0_L00?_I?_00?.fastq.gz
reports
output/Reports:file
Demultiplexing Reports
Reports/*.{csv,xml}
logs
output/Logs:file
Log files
Logs/*.{log,txt}
interop
**/InterOp/*.bin:file
Interop files
*.{bin}
versions
versions.yml:file
File containing software versions
versions.yml
