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
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
Demultiplexed sample FASTQ files
**_S*_L00?_R?_00?.fastq.gz
fastq_idx
output/**_S[1-9]*_I?_00?.fastq.gz
Optional demultiplexed index FASTQ files
**_S*_L00?_I?_00?.fastq.gz
undetermined
output/**Undetermined_S0*_R?_00?.fastq.gz
Optional undetermined sample FASTQ files
Undetermined_S0_L00?_R?_00?.fastq.gz
undetermined_idx
output/**Undetermined_S0*_I?_00?.fastq.gz
Optional undetermined index FASTQ files
Undetermined_S0_L00?_I?_00?.fastq.gz
reports
output/Reports
Demultiplexing Reports
Reports
stats
output/Stats
Statistics files
Stats
interop
InterOp/*.bin
Interop files
*.{bin}
xml
**/*.xml
Output XML files, for example RunInfo.xml
versions_bcl2fastq
${task.process}
:string
The name of the process
bcl2fastq
The name of the tool
bcl2fastq -V 2>&1 | grep -m 1 bcl2fastq | sed 's/^.*bcl2fastq v//'
:eval
The expression to obtain the version of the tool
versions
