workflows/ingestion/spaceranger_mapping

Description

A pipeline for running Space Ranger (4.1.0) mapping.

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input	file required multiple	The fastq.gz files to align. Can also be a single directory containing fastq.gz files. Individual FASTQ files should follow the naming convention of 10x Genomics: [Sample Name]_S[Sample Number]_L[Lane Number]_[Read Type]_001.fastq.gz Where: [Sample Name] is the name assigned during sample preparation/sequencing S[Sample Number] is the sample index (usually S1, S2, etc.) L[Lane Number] identifies the sequencing lane (L001, L002, etc.) [Read Type] will be one of: R1 - Read 1 (contains the spatial barcode and UMI) R2 - Read 2 (contains the actual cDNA sequence)
--gex_reference	file required	Path of folder containing 10x-compatible reference
--probe_set	file	CSV file specifying the probe set used. Required for probe-based assays (FFPE / standard Visium and Visium HD). Omit for Visium HD 3' data.
--cytaimage	file	Brightfield image generated by the CytAssist instrument. When using CytAssist workflow, either this or --image must be provided.
--image	file	H&E or fluorescence microscope image in TIFF or JPG format. Required for standard Visium workflow, optional when using --cytaimage for CytAssist workflow.

Name

Type & Properties

--id

string

required

--input

file

required

multiple

--gex_reference

file

required

--probe_set

file

--cytaimage

file

--image

file

Outputs

Name	Type & Properties	Description
--output_raw	file required output	Location where the output folder from Cell Ranger will be stored.
--output_h5mu	file required output	The output from Cell Ranger, converted to h5mu.
--output_type	string	Which Cell Ranger output to use for converting to h5mu.
--uns_metrics	string	Name of the .uns slot under which to QC metrics (if any).
--uns_probe_set	string	Name of the .uns slot under which to store probe set information (if any).
--obsm_coordinates	string	Name of the .obsm slot under which to store the cell centroid coordinates.
--output_compression	string	Compression to use when writing the h5mu file.

Name

Type & Properties

--output_raw

file

required

output

--output_h5mu

file

required

output

--output_type

string

--uns_metrics

string

--uns_probe_set

string

--obsm_coordinates

string

--output_compression

string

Image Options

Name	Type & Properties	Description
--darkimage	file	Multi-channel, dark-background fluorescence image
--colorizedimage	file	Color image representing pre-colored dark-background fluorescence images
--dapi_index	integer	Index of DAPI channel (1-indexed) of fluorescence image
--image_scale	double	Microns per microscope image pixel
--reorient_images	boolean	Whether to rotate and mirror image to align fiducial pattern
--loupe_alignment	file	Alignment file produced by the Loupe Browser manual alignment step. Overrides automatic fiducial and tissue detection. The image used to generate this file must match --image or --cytaimage.

Name

Type & Properties

--darkimage

file

--colorizedimage

file

--dapi_index

integer

--image_scale

double

--reorient_images

boolean

--loupe_alignment

file

Slide Information

Name	Type & Properties	Description
--slide	string	Visium slide serial number (e.g., 'V10J25-015')
--area	string	Visium capture area identifier (e.g., 'A1')
--unknown_slide	string	Use this option if the slide serial number and area were entered incorrectly on the CytAssist instrument and the correct values are unknown. Not compatible with --slide, --area, or --slide-file options
--slidefile	file	Slide design file for offline use
--override_id	boolean_true	Overrides the slide serial number and capture area provided in the Cytassist image metadata

Name

Type & Properties

--slide

string

--area

string

--unknown_slide

string

--slidefile

file

--override_id

boolean_true

SpaceRanger arguments

Name	Type & Properties	Description
--create_bam	boolean required	Enable or disable BAM file generation
--nosecondary	boolean_true	Disable secondary analysis (e.g., clustering)
--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
--filter_probes	boolean	Whether to filter the probe set using the "included" column
--custom_bin_size	integer	Bin Visium HD data to specified size in microns (4-100, even values only) in addition to the standard binning size (2 µm, 8 µm, 16 µm)
--include_introns	boolean	Include intronic reads in the count. When unset, Space Ranger applies its own default (true for Visium HD 3' and Visium v1, false otherwise).

Name

Type & Properties

--create_bam

boolean

required

--nosecondary

boolean_true

--r1_length

integer

--r2_length

integer

--filter_probes

boolean

--custom_bin_size

integer

--include_introns

boolean

Segmentation Options

Name	Type & Properties	Description
--nucleus_segmentation	boolean	Enable or disable nucleus and cell segmentation for Visium HD / HD 3' H&E samples. When unset, Space Ranger runs segmentation by default if an H&E image is provided.
--custom_segmentation_file	file	Custom nucleus segmentation mask to use instead of the built-in algorithm. Requires --nucleus_expansion_distance_micron.
--nucleus_expansion_distance_micron	double	Distance in microns to expand each nucleus to approximate the cell boundary.
--max_nucleus_diameter_px	integer	Maximum nucleus diameter in pixels, for samples with exceptionally large cells.
--umi_registration	boolean	Enable or disable UMI-based registration that aligns the microscope image to the UMI count data for Visium HD. When unset, Space Ranger applies its default.
--umi_to_image_offset	string	Supply a custom offset (as accepted by Space Ranger) to override UMI-to-image registration when automatic convergence is incorrect.

Name

Type & Properties

--nucleus_segmentation

boolean

--custom_segmentation_file

file

--nucleus_expansion_distance_micron

double

--max_nucleus_diameter_px

integer

--umi_registration

boolean

--umi_to_image_offset

string

Cell Annotation

Name	Type & Properties	Description
--cell_annotation_model	string	Cloud-based cell type annotation model to use (Visium HD / HD 3' only, requires segmentation), which requires --tenx_cloud_token_path. When left out, Space Ranger still annotates human samples with the bundled Pan-Human Azimuth model, which runs locally and needs no token.
--tenx_cloud_token_path	file	Path to a 10x Cloud token JSON, required for cloud-based annotation models.
--disable_cell_annotation	boolean_true	Disable cell type annotation.

Name

Type & Properties

--cell_annotation_model

string

--tenx_cloud_token_path

file

--disable_cell_annotation

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
output_raw: "$id.$key.output_raw.output_dir"  
output_h5mu: "$id.$key.output_h5mu.h5mu"  
output_type: [ "raw" ]  
uns_metrics: [ "metrics_summary" ]  
uns_probe_set: [ "probe_set" ]  
obsm_coordinates: [ "spatial" ]  
reorient_images: [ true ]  
create_bam: [ true ]  
filter_probes: [ true ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.6.0 \  
  -main-script target/nextflow/workflows/ingestion/spaceranger_mapping/main.nf \  
  -params-file params.yaml

workflows/ingestion/spaceranger_mapping

Inputs

Outputs

Image Options

Slide Information

SpaceRanger arguments

Segmentation Options

Cell Annotation

Run this component

Relationships

Used by

Uses