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Build branch build/main with version build_main (280b21f)

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Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-6h5zv

Source commit: 280b21fc21

Source message: deploy: 6840f3802d04d96d44f29d3cdbd31c62d144b14d
This commit is contained in:
CI
2025-07-24 15:39:45 +00:00
parent b59203a4af
commit 72b5c7c839
375 changed files with 191080 additions and 560 deletions
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261
target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml Normal file
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name: "from_xenium_to_spatialexperiment"
namespace: "convert"
version: "build_main"
authors:
- name: "Dorien Roosen"
roles:
- "author"
- "maintainer"
info:
role: "Core Team Member"
links:
email: "dorien@data-intuitive.com"
github: "dorien-er"
linkedin: "dorien-roosen"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Arguments"
arguments:
- type: "file"
name: "--input"
alternatives:
- "-i"
description: "Input Xenium Output Bundle"
info: null
example:
- "path/to/xenium_bundle"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--add_experiment_xenium"
description: "Whether to add xenium.experiment parameters to the metadata."
info: null
default:
- true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--add_parquet_paths"
description: "Whether to add parquet paths to the metadata. \nIf True, `transcripts.parquet`,\
\ `cell_boundaries.parquet`, `nucleus_boundaries.parquet` will be added to the\
\ metadata. \n"
info: null
default:
- true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--alternative_experiment_features"
description: "Feature names containing these strings will be moved to altExps(sxe)\
\ slots as separate SpatialExperiment objects."
info: null
default:
- "NegControlProbe"
- "UnassignedCodeword"
- "NegControlCodeword"
- "antisense"
- "BLANK"
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Output SpatialExperiment file"
info: null
example:
- "output.rds"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "r_script"
path: "script.R"
is_executable: true
- type: "file"
path: "nextflow_labels.config"
dest: "nextflow_labels.config"
description: "Creates a SpatialExperiment object from the downloaded unzipped Xenium\
\ Output Bundle directory\nfor 10x Genomics Xenium spatial gene expression data,\
\ and saves it as a SpatialExperiment object.\nThe constructor assumes the downloaded\
\ unzipped Xenium Output Bundle has the following structure:\n\nMandatory files\n\
· | — cell_feature_matrix.h5\n· | — cells.parquet\nOptional files, by default added\
\ to the metadata() as a list of paths (will be converted to parquet):\n· | — transcripts.parquet\n\
· | — cell_boundaries.parquet\n· | — nucleus_boundaries.parquet\n· | — experiment.xenium\n"
test_resources:
- type: "r_script"
path: "test.R"
is_executable: true
- type: "file"
path: "xenium_tiny"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
repositories:
- type: "github"
name: "openpipeline"
repo: "openpipelines-bio/openpipeline"
tag: "2.1.2"
- type: "vsh"
name: "openpipeline_incubator"
repo: "openpipeline_incubator"
tag: "build/main"
links:
repository: "https://github.com/openpipelines-bio/openpipeline_spatial"
docker_registry: "ghcr.io"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
label:
- "lowmem"
- "singlecpu"
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: "rocker/r2u:24.04"
target_registry: "images.viash-hub.com"
target_tag: "build_main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "libhdf5-dev"
- "libgeos-dev"
interactive: false
- type: "r"
bioc:
- "SpatialExperimentIO"
bioc_force_install: false
warnings_as_errors: true
test_setup:
- type: "r"
cran:
- "testthat"
bioc_force_install: false
warnings_as_errors: true
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/convert/from_xenium_to_spatialexperiment/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/convert/from_xenium_to_spatialexperiment"
executable: "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment"
viash_version: "0.9.4"
git_commit: "280b21fc21238c6e7b2e76089deffdef5d979b34"
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: "vsh"
name: "openpipeline_incubator"
repo: "openpipeline_incubator"
tag: "build/main"
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".resources += {path: '/src/workflows/utils/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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target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment Executable file
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target/executable/convert/from_xenium_to_spatialexperiment/nextflow_labels.config Normal file
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process {
// Default resources for components that hardly do any processing
memory = { 2.GB * task.attempt }
cpus = 1
// Retry for exit codes that have something to do with memory issues
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries = 3
maxMemory = null
// CPU resources
withLabel: singlecpu { cpus = 1 }
withLabel: lowcpu { cpus = 4 }
withLabel: midcpu { cpus = 10 }
withLabel: highcpu { cpus = 20 }
// Memory resources
withLabel: lowmem { memory = { get_memory( 50.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 50.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
// Disk space
// Nextflow apparently can't handle empty directives, i.e.
// withLabel: lowdisk {}
// so for that reason we have to add a dummy directive
withLabel: lowdisk {
dummyDirective = "dummyValue"
}
withLabel: middisk {
dummyDirective = "dummyValue"
}
withLabel: highdisk {
dummyDirective = "dummyValue"
}
withLabel: veryhighdisk {
dummyDirective = "dummyValue"
}
// NOTE: The above labels intentionally do not have an effect by default.
// The user should set the disk space requirements by adding the following
// to the compute environment:
//
// withLabel: lowdisk { disk = { 20.GB * task.attempt } }
// withLabel: middisk { disk = { 100.GB * task.attempt } }
// withLabel: highdisk { disk = { 200.GB * task.attempt } }
// withLabel: veryhighdisk { disk = { 500.GB * task.attempt } }
}
def get_memory(to_compare) {
if (!process.containsKey("maxMemory") || !process.maxMemory) {
return to_compare
}
try {
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
return process.maxMemory
}
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
return max_memory as nextflow.util.MemoryUnit
}
else {
return to_compare
}
} catch (all) {
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
System.exit(1)
}
}