CI
6ca529fc36
Build pipeline: openpipelines-bio.openpipeline-spatial.update-spatialdata-sdzfd
Source commit: a58c202dcc
Source message: update changelog
211 lines
7.1 KiB
YAML
211 lines
7.1 KiB
YAML
name: "spaceranger_mapping"
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namespace: "workflows/ingestion"
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scope: "public"
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description: "A pipeline for running SpaceRanger mapping."
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info:
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name: SpaceRanger mapping
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test_dependencies:
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- name: spaceranger_mapping_test
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namespace: test_workflows/ingestion
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authors:
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- __merge__: /src/authors/dorien_roosen.yaml
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roles: [ maintainer ]
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- __merge__: /src/authors/weiwei_schultz.yaml
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roles: [ contributor ]
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argument_groups:
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- name: Inputs
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arguments:
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- name: "--id"
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required: true
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type: string
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description: ID of the sample.
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example: foo
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- name: --input
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type: file
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required: true
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multiple: true
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description: |
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The fastq.gz files to align. Can also be a single directory containing fastq.gz files.
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Individual FASTQ files should follow the naming convention of 10x Genomics:
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[Sample Name]_S[Sample Number]_L[Lane Number]_[Read Type]_001.fastq.gz
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Where:
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[Sample Name] is the name assigned during sample preparation/sequencing
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S[Sample Number] is the sample index (usually S1, S2, etc.)
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L[Lane Number] identifies the sequencing lane (L001, L002, etc.)
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[Read Type] will be one of:
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R1 - Read 1 (contains the spatial barcode and UMI)
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R2 - Read 2 (contains the actual cDNA sequence)
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example: [ "sample_S1_L001_R1_001.fastq.gz", "sample_S1_L001_R2_001.fastq.gz" ]
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- name: --gex_reference
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type: file
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required: true
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description: Path of folder containing 10x-compatible reference
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example: "/path/to/refdata-gex-GRCh38-2020-A"
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- name: --probe_set
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type: file
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required: true
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description: CSV file specifying the probe set used
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example: "Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv"
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- name: --cytaimage
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type: file
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required: false
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description: |
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Brightfield image generated by the CytAssist instrument.
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When using CytAssist workflow, either this or --image must be provided.
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example: "cyta_image.tif"
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- name: --image
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type: file
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required: false
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description: |
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H&E or fluorescence microscope image in TIFF or JPG format.
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Required for standard Visium workflow, optional when using --cytaimage for CytAssist workflow.
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example: "brightfield.tif"
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- name: Outputs
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arguments:
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- name: "--output_raw"
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type: file
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direction: output
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description: "Location where the output folder from Cell Ranger will be stored."
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required: true
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example: output_dir/
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- name: "--output_h5mu"
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type: file
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direction: output
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description: "The output from Cell Ranger, converted to h5mu."
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required: true
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example: output.h5mu
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- name: "--output_type"
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type: string
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description: "Which Cell Ranger output to use for converting to h5mu."
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choices: [ raw, filtered ]
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default: raw
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- name: "--uns_metrics"
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type: string
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description: Name of the .uns slot under which to QC metrics (if any).
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default: "metrics_summary"
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- name: "--uns_probe_set"
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type: string
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description: Name of the .uns slot under which to store probe set information (if any).
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default: "probe_set"
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- name: "--obsm_coordinates"
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type: string
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description: Name of the .obsm slot under which to store the cell centroid coordinates.
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default: "spatial"
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- name: "--output_compression"
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type: string
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description: Compression to use when writing the h5mu file.
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choices: [ gzip, lzf ]
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- name: Image Options
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arguments:
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- name: --darkimage
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type: file
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description: Multi-channel, dark-background fluorescence image
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required: false
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example: "fluorescence.tif"
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- name: --colorizedimage
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type: file
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description: Color image representing pre-colored dark-background fluorescence images
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required: false
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example: "colored_fluorescence.tif"
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- name: --dapi_index
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type: integer
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description: Index of DAPI channel (1-indexed) of fluorescence image
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required: false
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example: 1
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min: 1
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- name: --image_scale
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type: double
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description: Microns per microscope image pixel
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required: false
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example: 0.65
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min: 0.01
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max: 10
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- name: --reorient_images
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type: boolean
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default: true
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description: Whether to rotate and mirror image to align fiducial pattern
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- name: Slide Information
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arguments:
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- name: --slide
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type: string
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description: Visium slide serial number (e.g., 'V10J25-015')
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required: false
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example: "V10J25-015"
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- name: --area
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type: string
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description: Visium capture area identifier (e.g., 'A1')
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required: false
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example: "A1"
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- name: --unknown_slide
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type: string
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description: |
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Use this option if the slide serial number and area were entered incorrectly on the CytAssist
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instrument and the correct values are unknown. Not compatible with --slide, --area, or
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--slide-file options
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required: false
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choices: [visium-1, visium-2, visium-2-large, visium-hd]
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- name: --slidefile
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type: file
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description: Slide design file for offline use
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required: false
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example: "slide_design.gpr"
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- name: --override_id
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type: boolean_true
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description: Overrides the slide serial number and capture area provided in the Cytassist image metadata
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- name: SpaceRanger arguments
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arguments:
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- name: --create_bam
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type: boolean
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required: true
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description: Enable or disable BAM file generation
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default: true
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- name: --nosecondary
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type: boolean_true
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description: Disable secondary analysis (e.g., clustering)
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- name: --r1_length
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type: integer
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required: false
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description: Hard trim the input Read 1 to this length before analysis
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min: 1
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- name: --r2_length
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type: integer
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required: false
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description: Hard trim the input Read 2 to this length before analysis
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min: 1
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- name: --filter_probes
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type: boolean
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default: true
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description: Whether to filter the probe set using the "included" column
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- name: --custom_bin_size
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type: integer
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description: 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)
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min: 4
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max: 100
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dependencies:
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- name: mapping/spaceranger_count
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- name: convert/from_spaceranger_to_h5mu
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resources:
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- type: nextflow_script
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path: main.nf
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entrypoint: run_wf
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- type: file
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path: /src/workflows/utils/
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test_resources:
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- type: nextflow_script
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path: test.nf
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entrypoint: test_wf
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- path: /resources_test/visium
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- path: /resources_test/GRCh38
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runners:
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- type: nextflow |