```
docker run --rm -it quay.io/nf-core/cellranger:9.0.1 \
  cellranger count --help
```

Count gene expression and/or feature barcode reads from a single sample and GEM
well

Usage: cellranger count [OPTIONS] --id <ID> --create-bam <true|false>

Options:
      --id <ID>
          A unique run id and output folder name [a-zA-Z0-9_-]+
      --description <TEXT>
          Sample description to embed in output files [default: ]
      --transcriptome <PATH>
          Path of folder containing 10x-compatible transcriptome reference
      --fastqs <PATH>
          Path to input FASTQ data
      --project <TEXT>
          Name of the project folder within a mkfastq or bcl2fastq-generated
          folder from which to pick FASTQs
      --sample <PREFIX>
          Prefix of the filenames of FASTQs to select
      --lanes <NUMS>
          Only use FASTQs from selected lanes
      --libraries <CSV>
          CSV file declaring input library data sources
      --feature-ref <CSV>
          Feature reference CSV file, declaring Feature Barcode constructs and
          associated barcodes
      --expect-cells <NUM>
          Expected number of recovered cells, used as input to cell calling
          algorithm
      --force-cells <NUM>
          Force pipeline to use this number of cells, bypassing cell calling
          algorithm. [MINIMUM: 10]
      --create-bam <true|false>
          Enable or disable BAM file generation. Setting --create-bam=false
          reduces the total computation time and the size of the output
          directory (BAM file not generated). We recommend setting
          --create-bam=true if unsure. See https://10xgen.com/create-bam for
          additional guidance [possible values: true, false]
      --nosecondary
          Disable secondary analysis, e.g. clustering. Optional
      --r1-length <NUM>
          Hard trim the input Read 1 to this length before analysis
      --r2-length <NUM>
          Hard trim the input Read 2 to this length before analysis
      --include-introns <true|false>
          Include intronic reads in count [default: true] [possible values:
          true, false]
      --chemistry <CHEM>
          Assay configuration. NOTE: by default the assay configuration is
          detected automatically, which is the recommended mode. You usually
          will not need to specify a chemistry. Options are: 'auto' for
          autodetection, 'threeprime' for Single Cell 3', 'fiveprime' for
          Single Cell 5', 'SC3Pv1' or 'SC3Pv2' or 'SC3Pv3' or 'SC3Pv4' for
          Single Cell 3' v1/v2/v3/v4, 'SC3Pv3LT' for Single Cell 3' v3 LT,
          'SC3Pv3HT' for Single Cell 3' v3 HT, 'SC5P-PE' or 'SC5P-PE-v3' or
          'SC5P-R2' or 'SC5P-R2-v3' for Single Cell 5', paired-end/R2-only,
          'SC-FB' for Single Cell Antibody-only 3' v2 or 5'. To analyze the GEX
          portion of multiome data, chemistry must be set to 'ARC-v1' [default:
          auto]
      --no-libraries
          Proceed with processing using a --feature-ref but no Feature Barcode
          libraries specified with the 'libraries' flag
      --check-library-compatibility <true|false>
          Whether to check for barcode compatibility between libraries.
          [default: true] [possible values: true, false]
      --tenx-cloud-token-path <PATH>
          The path to the 10x Cloud Analysis user token used to enable cell
          annotation. If not provided, will default to the location stored
          through cellranger cloud auth setup
      --cell-annotation-model <MODEL>
          Cell annotation model to use. Valid model names can be viewed by
          running `cellranger cloud annotation models` or on the 10x Genomics
          Support site (https://www.10xgenomics.com/support). If "auto", uses
          the default model for the species. If not provided, does not run cell
          annotation
      --min-crispr-umi <NUM>
          Minimum CRISPR UMI threshold [default: 3]
      --dry
          Do not execute the pipeline. Generate a pipeline invocation (.mro)
          file and stop
      --jobmode <MODE>
          Job manager to use. Valid options: local (default), sge, lsf, slurm or
          path to a .template file. Search for help on "Cluster Mode" at
          support.10xgenomics.com for more details on configuring the pipeline
          to use a compute cluster
      --localcores <NUM>
          Set max cores the pipeline may request at one time. Only applies to
          local jobs
      --localmem <NUM>
          Set max GB the pipeline may request at one time. Only applies to local
          jobs
      --localvmem <NUM>
          Set max virtual address space in GB for the pipeline. Only applies to
          local jobs
      --mempercore <NUM>
          Reserve enough threads for each job to ensure enough memory will be
          available, assuming each core on your cluster has at least this much
          memory available. Only applies to cluster jobmodes
      --maxjobs <NUM>
          Set max jobs submitted to cluster at one time. Only applies to cluster
          jobmodes
      --jobinterval <NUM>
          Set delay between submitting jobs to cluster, in ms. Only applies to
          cluster jobmodes
      --overrides <PATH>
          The path to a JSON file that specifies stage-level overrides for cores
          and memory. Finer-grained than --localcores, --mempercore and
          --localmem. Consult https://10xgen.com/resource-override for an
          example override file
      --output-dir <PATH>
          Output the results to this directory
      --uiport <PORT>
          Serve web UI at http://localhost:PORT
      --disable-ui
          Do not serve the web UI
      --noexit
          Keep web UI running after pipestance completes or fails
      --nopreflight
          Skip preflight checks
  -h, --help
          Print help
