cellranger/cellranger_count

cellranger

single-cell

rna-seq

alignment

count

Description

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

FASTQ inputs

Name	Type & Properties	Description
--fastqs	file required multiple	The fastq.gz files to align. Can also be a single directory containing fastq.gz files.
--description	string	Sample description to embed in output files
--sample	string	Prefix of the filenames of FASTQs to select
--lanes	integer multiple	Only use FASTQs from selected lanes.
--libraries	file	CSV file declaring input library data sources

Name

Type & Properties

--fastqs

file

required

multiple

--description

string

--sample

string

--lanes

integer

multiple

--libraries

file

Reference inputs

Name	Type & Properties	Description
--transcriptome	file required	Path of folder containing 10x-compatible transcriptome reference. Can also be a `.tar.gz` file.
--feature_ref	file	Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes

Name

Type & Properties

--transcriptome

file

required

--feature_ref

file

Analysis settings

Name	Type & Properties	Description
--expect_cells	integer	Expected number of recovered cells, used as input to cell calling algorithm.
--force_cells	integer	Force pipeline to use this number of cells, bypassing cell calling algorithm. Minimum: 10.
--r1_length	integer	Hard trim the input Read 1 to this length before analysis
--r2_length	integer	Hard trim the input Read 2 to this length before analysis
--include_introns	boolean_true	Include intronic reads in count. Default: true.
--chemistry	string	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'`. See the [10x Genomics FAQ](https://kb.10xgenomics.com/hc/en-us/articles/115003764132-How-does-Cell-Ranger-auto-detect-chemistry-) for more information on how chemistry is detected.
--cell_annotation_model	string	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	integer	Minimum CRISPR UMI threshold. Default: 3.

Name

Type & Properties

--expect_cells

integer

--force_cells

integer

--r1_length

integer

--r2_length

integer

--include_introns

boolean_true

--chemistry

string

--cell_annotation_model

string

--min_crispr_umi

integer

Outputs

Name	Type & Properties	Description
--output	file required output	The folder to store the alignment results.
--create_bam	boolean_true	Enable or disable BAM file generation. Setting this to false reduces the total computation time and the size of the output directory (BAM file not generated). We recommend setting it to true if unsure. See https://10xgen.com/create-bam for additional guidance.
--no_secondary	boolean_true	Disable secondary analysis, e.g. clustering.

Name

Type & Properties

--output

file

required

output

--create_bam

boolean_true

--no_secondary

boolean_true

Additional arguments

Name	Type & Properties	Description
--no_libraries	boolean_true	Proceed with processing using a `--feature_ref` but no Feature Barcode libraries specified with the 'libraries' flag.
--check_library_compatibility	boolean_true	Whether to check for barcode compatibility between libraries.
--tenx_cloud_token	file	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.
--dry	boolean_true	Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop.

Name

Type & Properties

--no_libraries

boolean_true

--check_library_compatibility

boolean_true

--tenx_cloud_token

file

--dry

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/cellranger/cellranger_count/main.nf \  
  -params-file params.yaml

cellranger/cellranger_count

FASTQ inputs

Reference inputs

Analysis settings

Outputs

Additional arguments

Run this component

Relationships

Used by

Uses