Demultiplex Illumina BCL files
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
samplesheet{:bash}
:file
Input samplesheet
*.{csv}
run_dir{:bash}
Input run directory containing RunInfo.xml and BCL data Could be a directory or a tar of the directory
fastq{:bash}
Groovy Map containing sample information
output/**_S[1-9]*_R?_00?.fastq.gz{:bash}
Demultiplexed sample FASTQ files
**_S*_L00?_R?_00?.fastq.gz
fastq_idx{:bash}
output/**_S[1-9]*_I?_00?.fastq.gz{:bash}
Optional demultiplexed index FASTQ files
**_S*_L00?_I?_00?.fastq.gz
undetermined{:bash}
output/**Undetermined_S0*_R?_00?.fastq.gz{:bash}
Optional undetermined sample FASTQ files
Undetermined_S0_L00?_R?_00?.fastq.gz
undetermined_idx{:bash}
output/**Undetermined_S0*_I?_00?.fastq.gz{:bash}
Optional undetermined index FASTQ files
Undetermined_S0_L00?_I?_00?.fastq.gz
reports{:bash}
output/Reports{:bash}
Demultiplexing Reports
Reports
stats{:bash}
output/Stats{:bash}
Statistics files
Stats
interop{:bash}
InterOp/*.bin{:bash}
Interop files
*.{bin}
versions_bcl2fastq{:bash}
${task.process}{:bash}
:string
The name of the process
bcl2fastq{:bash}
The name of the tool
bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
