workflows/ingestion/spaceranger_mapping

Description

A pipeline for running SpaceRanger 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 required	CSV file specifying the probe set used
--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

required

--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

Name

Type & Properties

--darkimage

file

--colorizedimage

file

--dapi_index

integer

--image_scale

double

--reorient_images

boolean

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)

Name

Type & Properties

--create_bam

boolean

required

--nosecondary

boolean_true

--r1_length

integer

--r2_length

integer

--filter_probes

boolean

--custom_bin_size

integer

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 v0.3.0 \  
  -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

Run this component

Relationships

Used by

Uses