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openpipeline_spatial/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml
CI b59203a4af Build branch build/main with version build_main (6ae6ad1) 
Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-h86dl

Source commit: 6ae6ad1936

Source message: deploy: 00cafd63af52decfa15830ba20bc88f7a9384965
2025-07-10 14:46:24 +00:00

466 lines
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YAML
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name: "spaceranger_count"
namespace: "mapping"
version: "build_main"
authors:
- name: "Jakub Majercik"
roles:
- "author"
info:
role: "Contributor"
links:
email: "jakub@data-intuitive.com"
github: "jakubmajercik"
linkedin: "jakubmajercik"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Bioinformatics Engineer"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--gex_reference"
description: "Path of folder containing 10x-compatible reference"
info: null
example:
- "/path/to/refdata-gex-GRCh38-2020-A"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--input"
description: "Path to a directory containing input FASTQ data. Individual FASTQ\
\ files should follow the naming convention of 10x Genomics:\n[Sample Name]_S[Sample\
\ Number]_L[Lane Number]_[Read Type]_001.fastq.gz\n\nWhere:\n[Sample Name] is\
\ the name assigned during sample preparation/sequencing\nS[Sample Number] is\
\ the sample index (usually S1, S2, etc.)\nL[Lane Number] identifies the sequencing\
\ lane (L001, L002, etc.)\n\n[Read Type] will be one of:\nR1 - Read 1 (contains\
\ the spatial barcode and UMI)\nR2 - Read 2 (contains the actual cDNA sequence)\n\
I1 - Index Read 1 (if applicable)\nI2 - Index Read 2 (if applicable)\n"
info: null
example:
- "/path/to/fastq_folder"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--probe_set"
description: "CSV file specifying the probe set used"
info: null
example:
- "Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--cytaimage"
description: "Brightfield image generated by the CytAssist instrument. \nWhen\
\ using CytAssist workflow, either this or --image must be provided.\n"
info: null
example:
- "cyta_image.tif"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--image"
description: "H&E or fluorescence microscope image in TIFF or JPG format. \nRequired\
\ for standard Visium workflow, optional when using --cytaimage for CytAssist\
\ workflow.\n"
info: null
example:
- "brightfield.tif"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
description: "The folder to store the alignment results"
info: null
example:
- "/path/to/output"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Slide Information"
arguments:
- type: "string"
name: "--slide"
description: "Visium slide serial number (e.g., 'V10J25-015')"
info: null
example:
- "V10J25-015"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--area"
description: "Visium capture area identifier (e.g., 'A1')"
info: null
example:
- "A1"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--unknown_slide"
description: "Use this option if the slide serial number and area were entered\
\ incorrectly on the CytAssist \ninstrument and the correct values are unknown.\
\ Not compatible with --slide, --area, or \n--slide-file options\n"
info: null
required: false
choices:
- "visium-1"
- "visium-2"
- "visium-2-large"
- "visium-hd"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--slidefile"
description: "Slide design file for offline use"
info: null
example:
- "slide_design.gpr"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--override_id"
description: "Overrides the slide serial number and capture area provided in the\
\ Cytassist image metadata"
info: null
direction: "input"
- name: "Image Options"
arguments:
- type: "file"
name: "--darkimage"
description: "Multi-channel, dark-background fluorescence image"
info: null
example:
- "fluorescence.tif"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--colorizedimage"
description: "Color image representing pre-colored dark-background fluorescence\
\ images"
info: null
example:
- "colored_fluorescence.tif"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--dapi_index"
description: "Index of DAPI channel (1-indexed) of fluorescence image"
info: null
example:
- 1
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--image_scale"
description: "Microns per microscope image pixel"
info: null
example:
- 0.65
required: false
min: 0.01
max: 10.0
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--reorient_images"
description: "Whether to rotate and mirror image to align fiducial pattern"
info: null
default:
- true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Processing Options"
arguments:
- type: "boolean"
name: "--create_bam"
description: "Enable or disable BAM file generation"
info: null
default:
- true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--nosecondary"
description: "Disable secondary analysis (e.g., clustering)"
info: null
direction: "input"
- type: "integer"
name: "--r1_length"
description: "Hard trim the input Read 1 to this length before analysis"
info: null
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--r2_length"
description: "Hard trim the input Read 2 to this length before analysis"
info: null
required: false
min: 1
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--filter_probes"
description: "Whether to filter the probe set using the \"included\" column"
info: null
default:
- true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--custom_bin_size"
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)"
info: null
required: false
min: 4
max: 100
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Input Selection"
arguments:
- type: "string"
name: "--project"
description: "Project folder name within mkfastq output"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--sample"
description: "Prefix of FASTQ filenames to select"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--lanes"
description: "Only use FASTQs from selected lanes"
info: null
example:
- 1
- 2
- 3
required: false
direction: "input"
multiple: true
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "Count gene expression and protein expression reads from a single capture\
\ area."
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "visium"
- type: "file"
path: "GRCh38"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
repositories:
- type: "github"
name: "openpipeline"
repo: "openpipelines-bio/openpipeline"
tag: "2.1.2"
- type: "github"
name: "openpipeline_incubator"
repo: "openpipelines-bio/openpipeline_incubator"
tag: "main"
keywords:
- "spaceranger"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
docker_registry: "ghcr.io"
documentation: "https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/space-ranger-count"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
script:
- "includeConfig(\"nextflow_labels.config\")"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "ghcr.io/data-intuitive/spaceranger:3.1"
target_registry: "images.viash-hub.com"
target_tag: "build_main"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "DEBIAN_FRONTEND=noninteractive apt update && \\\napt upgrade -y && apt install\
\ -y procps && rm -rf /var/lib/apt/lists/*\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/mapping/spaceranger_count/config.vsh.yaml"
runner: "nextflow"
engine: "docker|native"
output: "target/nextflow/mapping/spaceranger_count"
executable: "target/nextflow/mapping/spaceranger_count/main.nf"
viash_version: "0.9.3"
git_commit: "6ae6ad193664a12a39c23f20030ebf03d9e886c6"
git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial"
package_config:
name: "openpipeline_spatial"
version: "build_main"
info:
test_resources:
- type: "s3"
path: "s3://openpipelines-bio/openpipeline_spatial/resources_test"
dest: "resources_test"
repositories:
- type: "github"
name: "openpipeline"
repo: "openpipelines-bio/openpipeline"
tag: "2.1.2"
- type: "github"
name: "openpipeline_incubator"
repo: "openpipelines-bio/openpipeline_incubator"
tag: "main"
viash_version: "0.9.3"
source: "src"
target: "target"
config_mods:
- ".resources += {path: '/src/labels.config', dest: 'nextflow_labels.config'}\n\
.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
)'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'build_main'"
organization: "vsh"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
docker_registry: "ghcr.io"
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