Module to use Cell Ranger’s pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.


Name (Type)

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end


reads (file)

List of input FastQ files. The order of the input files MUST be [“sample1 R1”, “sample1 R2”, “sample2, R1”,
“sample2, R2”, …]. This can usually be achieved by sorting the input files by file name.

Background: 10x data is always paired-end with R1 containing cell barcode and UMI
and R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name
convention: ${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz. This module automatically
renames files to match this convention based on the order of input files to avoid various
issues (see To avoid mistakes, the module
throws an error if a pair of R1 and R2 fastq files does not have the same filename except for the “_R1”/“_R2” part.
Renaming the files does not affect the results (see for detailed tests).


reference (directory)

Folder containing all the reference indices needed by Cell Ranger


Name (Type)

outs (file)

Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list


versions (file)

File containing software version



10x Genomics EULA

Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.