mapping/cellranger_count

Description

Align fastq files using Cell Ranger count.

Inputs

Name	Type & Properties	Description
--input	file required multiple	The fastq.gz files to align. Can also be a single directory containing fastq.gz files.
--reference	file required	The path to Cell Ranger reference tar.gz file. Can also be a directory.
--feature_reference	file	Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes

Name

Type & Properties

--input

file

required

multiple

--reference

file

required

--feature_reference

file

Outputs

Name	Type & Properties	Description
--output	file required output	The folder to store the alignment results.

Name

Type & Properties

--output

file

required

output

Arguments

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.
--chemistry	string	Assay configuration. - auto: autodetect mode - threeprime: Single Cell 3' - fiveprime: Single Cell 5' - SC3Pv1: Single Cell 3' v1 NOTE: this mode cannot be auto-detected. It must be set explicitly with this option. - SC3Pv2: Single Cell 3' v2 - SC3Pv3: Single Cell 3' v3 - SC3Pv4: Single Cell 3' v4 - SC3Pv3LT: Single Cell 3' v3 LT - SC3Pv3HT: Single Cell 3' v3 HT - SC5P-R2-v3: Single Cell 5', paired-end/R2-only - SC5P-PE-v3: Single Cell 5' paired-end v3 (GEM-X) - SC5P-PE: Single Cell 5' paired-end - SC5P-R2: Single Cell 5' R2-only - SC-FB: Single Cell Antibody-only 3' v2 or 5' - ARC-v1: for analyzing the Gene Expression portion of Multiome data. NOTE: when the pipeline auto-detects ARC-v1 chemistry, an error is triggered. See https://kb.10xgenomics.com/hc/en-us/articles/115003764132-How-does-Cell-Ranger-auto-detect-chemistry- for more information.
--tenx_cloud_token_path	file	The 10x Cloud Analysis user token used to enable cell annotation.
--cell_annotation_model	string	"Cell annotation model to use. If auto, uses the default model for the species. If not given, does not run cell annotation."
--secondary_analysis	boolean	Whether or not to run the secondary analysis e.g. clustering.
--generate_bam	boolean	Whether to generate a BAM file.
--include_introns	boolean	Include intronic reads in count.
--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
--lanes	integer multiple	Only use FASTQs from selected lanes.
--library_compatibility_check	boolean	Whether to check for barcode compatibility between libraries.
--min_crispr_umi	integer	Set the minimum number of CRISPR guide RNA UMIs required for protospacer detection. If a lower or higher sensitivity is desired for detection, this value can be customized according to specific experimental needs. Applicable only to datasets that include a CRISPR Guide Capture library.

Name

Type & Properties

--expect_cells

integer

--force_cells

integer

--chemistry

string

--tenx_cloud_token_path

file

--cell_annotation_model

string

--secondary_analysis

boolean

--generate_bam

boolean

--include_introns

boolean

--r1_length

integer

--r2_length

integer

--lanes

integer

multiple

--library_compatibility_check

boolean

--min_crispr_umi

integer

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output./path/to/output"  
chemistry: [ "auto" ]  
secondary_analysis: [ false ]  
generate_bam: [ true ]  
include_introns: [ true ]  
library_compatibility_check: [ true ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/mapping/cellranger_count/main.nf \  
  -params-file params.yaml

mapping/cellranger_count

Inputs

Outputs

Arguments

Run this component

Relationships

Used by

Uses