name: cellranger_count
description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression.
keywords:
  - align
  - count
  - reference
tools:
  - cellranger:
      description: 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.
      homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
      documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
      tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov

      licence: 10x Genomics EULA
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        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}_${R1,R2}_001.fastq.gz`. This module automatically
        renames files to match this convention based on the order of input files to avoid various
        issues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module
        throws an error if a pair of R1 and R2 fastq files does not have the same filename except for the "_R1"/"_R2" part.
        Renaming the files does not affect the results (see README.md for detailed tests).
      pattern: "*{R1,R2}*.fastq.gz"
  - reference:
      type: directory
      description: Folder containing all the reference indices needed by Cell Ranger
output:
  - outs:
      type: file
      description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list
      pattern: "${meta.id}/outs/*"
  - versions:
      type: file
      description: File containing software version
      pattern: "versions.yml"
authors:
  - "@ggabernet"
  - "@Emiller88"
