Matrix to Cell Ranger matrix module

This module allow to create a Cell Ranger matrix (version 1 or 2) from expression or matrix data.

  • Internal name: matrix2cellrangermatrix
  • Available: Only in local mode

  • Input port:
    • additionalannotation: Additional annotation data (format: additional_annotation_tsv) from the design file. This data allow to describe the genes/features of the Bioconductor SingleCellExperiment object
    • matrix: Matrix data (format: expression_matrix_tsv) if matrix input is enabled
    • expression: Expression step output (format: expression_results_tsv) if matrix input is not enabled

  • Output port: A Cell Ranger matrix.

  • Optional parameters:
    • Parameter Type Description Default value
    input.matrices boolean The input of the module is a matrix (e.g. 10X Genomics data). For SmartSeq2, this parameter is usually set to false. true
    use.additional.annotation boolean When this parameter is enabled, feature annotations will be used for the second column of the feature/gene file of the Cell Ranger matrix output. true
    additional.annotation.field.name string The name of the field in the additional annotation to use for the second column of the feature/gene file of the Cell Ranger matrix output. Gene name
    additional.annotation.type string Value of the third column of the feature file of the Cell Ranger matrix output (Cell Ranger matrix format version 2 only). Gene Expression.
    cell.ranger.matrix.format integer Version of the Cell Ranger format output to use. Currently only version 1 (Cell Ranger version 1 and 2) and 2 (Cell Ranger version 3) are supported. 2

  • Configuration example:
    • <!--  Matrix to Cell Ranger matrix step -->
<step id="mymatrix2cellrangermatrix" skip="false" discardoutput="false">
        <module>matrix2cellrangermatrix</module>
        <parameters>
                <parameter>
                        <name>input.matrices</name>
                        <value>true</value>
                </parameter>
                <parameter>
                        <name>use.additional.annotation</name>
                        <value>true</value>
                </parameter>
                <parameter>
                        <name>additional.annotation.field.name</name>
                        <value>Gene name</value>
                </parameter>
                <parameter>
                        <name>additional.annotation.type</name>
                        <value>Gene Expression</value>
                </parameter>
                <parameter>
                        <name>cell.ranger.matrix.format</name>
                        <value>2</value>
                </parameter>
        </parameters>
</step>