Build branch fix-integration-tests with version fix-integration-tests (da62b4ff)
Build pipeline: vsh-ci-dev-gckj5
Source commit: da62b4ffe3
Source message: Add labels to qc_test component
This commit is contained in:
333
target/executable/neighbors/bbknn/.config.vsh.yaml
Normal file
333
target/executable/neighbors/bbknn/.config.vsh.yaml
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@@ -0,0 +1,333 @@
|
||||
name: "bbknn"
|
||||
namespace: "neighbors"
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||||
version: "fix-integration-tests"
|
||||
authors:
|
||||
- name: "Dries De Maeyer"
|
||||
roles:
|
||||
- "author"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "ddemaeyer@gmail.com"
|
||||
github: "ddemaeyer"
|
||||
linkedin: "dries-de-maeyer-b46a814"
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||||
organizations:
|
||||
- name: "Janssen Pharmaceuticals"
|
||||
href: "https://www.janssen.com"
|
||||
role: "Principal Scientist"
|
||||
- name: "Dries Schaumont"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "dries@data-intuitive.com"
|
||||
github: "DriesSchaumont"
|
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orcid: "0000-0002-4389-0440"
|
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linkedin: "dries-schaumont"
|
||||
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 h5mu file"
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obsm_input"
|
||||
description: "The dimensionality reduction in `.obsm` to use for neighbour detection.\
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\ Defaults to X_pca."
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info: null
|
||||
default:
|
||||
- "X_pca"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obs_batch"
|
||||
description: ".obs column name discriminating between your batches."
|
||||
info: null
|
||||
default:
|
||||
- "batch"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
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||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output .h5mu file."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
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must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
info: null
|
||||
example:
|
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- "gzip"
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||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
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||||
direction: "input"
|
||||
multiple: false
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||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--uns_output"
|
||||
description: "Mandatory .uns slot to store various neighbor output objects."
|
||||
info: null
|
||||
default:
|
||||
- "neighbors"
|
||||
required: false
|
||||
direction: "input"
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||||
multiple: false
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||||
multiple_sep: ";"
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||||
- type: "string"
|
||||
name: "--obsp_distances"
|
||||
description: "In which .obsp slot to store the distance matrix between the resulting\
|
||||
\ neighbors."
|
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info: null
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||||
default:
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||||
- "distances"
|
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required: false
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||||
direction: "input"
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||||
multiple: false
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||||
multiple_sep: ";"
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||||
- type: "string"
|
||||
name: "--obsp_connectivities"
|
||||
description: "In which .obsp slot to store the connectivities matrix between the\
|
||||
\ resulting neighbors."
|
||||
info: null
|
||||
default:
|
||||
- "connectivities"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--n_neighbors_within_batch"
|
||||
description: "How many top neighbours to report for each batch; total number of\
|
||||
\ neighbours in the initial k-nearest-neighbours computation will be this number\
|
||||
\ times the number of batches."
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||||
info: null
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||||
default:
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||||
- 3
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||||
required: false
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||||
direction: "input"
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||||
multiple: false
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||||
multiple_sep: ";"
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||||
- type: "integer"
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||||
name: "--n_pcs"
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||||
description: "How many dimensions (in case of PCA, principal components) to use\
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||||
\ in the analysis."
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||||
info: null
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||||
default:
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||||
- 50
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||||
required: false
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||||
direction: "input"
|
||||
multiple: false
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||||
multiple_sep: ";"
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||||
- type: "integer"
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||||
name: "--n_trim"
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||||
description: "Trim the neighbours of each cell to these many top connectivities.\
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||||
\ May help with population independence and improve the tidiness of clustering.\
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||||
\ The lower the value the more independent the individual populations, at the\
|
||||
\ cost of more conserved batch effect. If `None` (default), sets the parameter\
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||||
\ value automatically to 10 times `neighbors_within_batch` times the number\
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||||
\ of batches. Set to 0 to skip."
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info: null
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||||
required: false
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||||
direction: "input"
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||||
multiple: false
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||||
multiple_sep: ";"
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||||
resources:
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- type: "python_script"
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path: "script.py"
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is_executable: true
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- type: "file"
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path: "nextflow_labels.config"
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dest: "nextflow_labels.config"
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||||
description: "BBKNN network generation\n"
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test_resources:
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||||
- type: "python_script"
|
||||
path: "test.py"
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||||
is_executable: true
|
||||
- type: "file"
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||||
path: "pbmc_1k_protein_v3_mms.h5mu"
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||||
- type: "file"
|
||||
path: "openpipelinetestutils"
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||||
dest: "openpipelinetestutils"
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info: null
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||||
status: "enabled"
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||||
links:
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repository: "https://github.com/openpipelines-bio/openpipeline"
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||||
docker_registry: "ghcr.io"
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||||
runners:
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||||
- type: "executable"
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||||
id: "executable"
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||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
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id: "nextflow"
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||||
directives:
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||||
label:
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||||
- "lowcpu"
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||||
- "highmem"
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||||
tag: "$id"
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||||
auto:
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||||
simplifyInput: true
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||||
simplifyOutput: false
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||||
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: "python:3.10-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "fix-integration-tests"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
- "build-essential"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "scanpy~=1.9.6"
|
||||
- "bbknn"
|
||||
- "scikit-learn~=1.2.2"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/neighbors/bbknn/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/neighbors/bbknn"
|
||||
executable: "target/executable/neighbors/bbknn/bbknn"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "da62b4ffe30b6ef36fcb7ef5944f29d45d1138ff"
|
||||
git_remote: "https://x-access-token:ghs_WgbTvvspBKMSQ5BPucz45vMfHrxqK54Vys9e@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1939-gda62b4ff"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "fix-integration-tests"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'fix-integration-tests'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
1364
target/executable/neighbors/bbknn/bbknn
Executable file
1364
target/executable/neighbors/bbknn/bbknn
Executable file
File diff suppressed because it is too large
Load Diff
42
target/executable/neighbors/bbknn/nextflow_labels.config
Normal file
42
target/executable/neighbors/bbknn/nextflow_labels.config
Normal file
@@ -0,0 +1,42 @@
|
||||
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
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.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)
|
||||
}
|
||||
}
|
||||
382
target/executable/neighbors/find_neighbors/.config.vsh.yaml
Normal file
382
target/executable/neighbors/find_neighbors/.config.vsh.yaml
Normal file
@@ -0,0 +1,382 @@
|
||||
name: "find_neighbors"
|
||||
namespace: "neighbors"
|
||||
version: "fix-integration-tests"
|
||||
authors:
|
||||
- name: "Dries De Maeyer"
|
||||
roles:
|
||||
- "maintainer"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "ddemaeyer@gmail.com"
|
||||
github: "ddemaeyer"
|
||||
linkedin: "dries-de-maeyer-b46a814"
|
||||
organizations:
|
||||
- name: "Janssen Pharmaceuticals"
|
||||
href: "https://www.janssen.com"
|
||||
role: "Principal Scientist"
|
||||
- name: "Robrecht Cannoodt"
|
||||
roles:
|
||||
- "contributor"
|
||||
info:
|
||||
role: "Core Team Member"
|
||||
links:
|
||||
email: "robrecht@data-intuitive.com"
|
||||
github: "rcannood"
|
||||
orcid: "0000-0003-3641-729X"
|
||||
linkedin: "robrechtcannoodt"
|
||||
organizations:
|
||||
- name: "Data Intuitive"
|
||||
href: "https://www.data-intuitive.com"
|
||||
role: "Data Science Engineer"
|
||||
- name: "Open Problems"
|
||||
href: "https://openproblems.bio"
|
||||
role: "Core Member"
|
||||
argument_groups:
|
||||
- name: "Arguments"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--input"
|
||||
alternatives:
|
||||
- "-i"
|
||||
description: "Input h5mu file"
|
||||
info: null
|
||||
example:
|
||||
- "input.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--modality"
|
||||
info: null
|
||||
default:
|
||||
- "rna"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obsm_input"
|
||||
description: "Which .obsm slot to use as a starting PCA embedding."
|
||||
info: null
|
||||
default:
|
||||
- "X_pca"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--output"
|
||||
alternatives:
|
||||
- "-o"
|
||||
description: "Output h5mu file containing the found neighbors."
|
||||
info: null
|
||||
example:
|
||||
- "output.h5mu"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "output"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--output_compression"
|
||||
description: "The compression format to be used on the output h5mu object."
|
||||
info: null
|
||||
example:
|
||||
- "gzip"
|
||||
required: false
|
||||
choices:
|
||||
- "gzip"
|
||||
- "lzf"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--uns_output"
|
||||
description: "Mandatory .uns slot to store various neighbor output objects."
|
||||
info: null
|
||||
default:
|
||||
- "neighbors"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obsp_distances"
|
||||
description: "In which .obsp slot to store the distance matrix between the resulting\
|
||||
\ neighbors."
|
||||
info: null
|
||||
default:
|
||||
- "distances"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obsp_connectivities"
|
||||
description: "In which .obsp slot to store the connectivities matrix between the\
|
||||
\ resulting neighbors."
|
||||
info: null
|
||||
default:
|
||||
- "connectivities"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--metric"
|
||||
description: "The distance metric to be used in the generation of the nearest\
|
||||
\ neighborhood network."
|
||||
info: null
|
||||
default:
|
||||
- "euclidean"
|
||||
required: false
|
||||
choices:
|
||||
- "cityblock"
|
||||
- "cosine"
|
||||
- "euclidean"
|
||||
- "l1"
|
||||
- "l2"
|
||||
- "manhattan"
|
||||
- "braycurtis"
|
||||
- "canberra"
|
||||
- "chebyshev"
|
||||
- "correlation"
|
||||
- "dice"
|
||||
- "hamming"
|
||||
- "jaccard"
|
||||
- "kulsinski"
|
||||
- "mahalanobis"
|
||||
- "minkowski"
|
||||
- "rogerstanimoto"
|
||||
- "russellrao"
|
||||
- "seuclidean"
|
||||
- "sokalmichener"
|
||||
- "sokalsneath"
|
||||
- "sqeuclidean"
|
||||
- "yule"
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--num_neighbors"
|
||||
description: "The size of local neighborhood (in terms of number of neighboring\
|
||||
\ data points) used for manifold approximation. Larger values result in more\
|
||||
\ global views of the manifold, while smaller values result in more local data\
|
||||
\ being preserved. In general values should be in the range 2 to 100. If knn\
|
||||
\ is True, number of nearest neighbors to be searched. If knn is False, a Gaussian\
|
||||
\ kernel width is set to the distance of the n_neighbors neighbor."
|
||||
info: null
|
||||
default:
|
||||
- 15
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--seed"
|
||||
description: "A random seed."
|
||||
info: null
|
||||
default:
|
||||
- 0
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obsm_knn_indices"
|
||||
description: "In which .obsm slot to store the indices of the k-nearest neighbors."
|
||||
info: null
|
||||
default:
|
||||
- "knn_indices"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--obsm_knn_distances"
|
||||
description: "In which .obsm slot to store the distances of the k-nearest neighbors."
|
||||
info: null
|
||||
default:
|
||||
- "knn_distances"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "setup_logger.py"
|
||||
- type: "file"
|
||||
path: "nextflow_labels.config"
|
||||
dest: "nextflow_labels.config"
|
||||
description: "Compute a neighborhood graph of observations [McInnes18].\n\nThe neighbor\
|
||||
\ search efficiency of this heavily relies on UMAP [McInnes18], which also provides\
|
||||
\ a method for estimating connectivities of data points - the connectivity of the\
|
||||
\ manifold (method=='umap'). If method=='gauss', connectivities are computed according\
|
||||
\ to [Coifman05], in the adaption of [Haghverdi16].\n"
|
||||
test_resources:
|
||||
- type: "python_script"
|
||||
path: "test.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "pbmc_1k_protein_v3"
|
||||
- type: "file"
|
||||
path: "openpipelinetestutils"
|
||||
dest: "openpipelinetestutils"
|
||||
info: null
|
||||
status: "enabled"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
runners:
|
||||
- type: "executable"
|
||||
id: "executable"
|
||||
docker_setup_strategy: "ifneedbepullelsecachedbuild"
|
||||
- type: "nextflow"
|
||||
id: "nextflow"
|
||||
directives:
|
||||
label:
|
||||
- "lowcpu"
|
||||
- "midmem"
|
||||
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: "python:3.10-slim"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "fix-integration-tests"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "procps"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "anndata==0.10.8"
|
||||
- "mudata~=0.2.4"
|
||||
- "pandas!=2.1.2"
|
||||
- "numpy<2.0.0"
|
||||
- "scanpy~=1.9.6"
|
||||
upgrade: true
|
||||
test_setup:
|
||||
- type: "docker"
|
||||
copy:
|
||||
- "openpipelinetestutils /opt/openpipelinetestutils"
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "/opt/openpipelinetestutils"
|
||||
upgrade: true
|
||||
- type: "python"
|
||||
user: false
|
||||
packages:
|
||||
- "viashpy==0.8.0"
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
id: "native"
|
||||
build_info:
|
||||
config: "src/neighbors/find_neighbors/config.vsh.yaml"
|
||||
runner: "executable"
|
||||
engine: "docker|native"
|
||||
output: "target/executable/neighbors/find_neighbors"
|
||||
executable: "target/executable/neighbors/find_neighbors/find_neighbors"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "da62b4ffe30b6ef36fcb7ef5944f29d45d1138ff"
|
||||
git_remote: "https://x-access-token:ghs_WgbTvvspBKMSQ5BPucz45vMfHrxqK54Vys9e@github.com/openpipelines-bio/openpipeline"
|
||||
git_tag: "0.2.0-1939-gda62b4ff"
|
||||
package_config:
|
||||
name: "openpipeline"
|
||||
version: "fix-integration-tests"
|
||||
info:
|
||||
test_resources:
|
||||
- type: "s3"
|
||||
path: "s3://openpipelines-data"
|
||||
dest: "resources_test"
|
||||
viash_version: "0.9.0"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
|
||||
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
|
||||
.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
|
||||
\ := 'includeConfig(\"nextflow_labels.config\")'\n"
|
||||
- ".engines += { type: \"native\" }"
|
||||
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
|
||||
- ".engines[.type == 'docker'].target_tag := 'fix-integration-tests'"
|
||||
organization: "vsh"
|
||||
links:
|
||||
repository: "https://github.com/openpipelines-bio/openpipeline"
|
||||
docker_registry: "ghcr.io"
|
||||
homepage: "https://openpipelines.bio"
|
||||
documentation: "https://openpipelines.bio/fundamentals"
|
||||
issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
|
||||
1432
target/executable/neighbors/find_neighbors/find_neighbors
Executable file
1432
target/executable/neighbors/find_neighbors/find_neighbors
Executable file
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,42 @@
|
||||
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
|
||||
|
||||
// Resource labels
|
||||
withLabel: singlecpu { cpus = 1 }
|
||||
withLabel: lowcpu { cpus = 4 }
|
||||
withLabel: midcpu { cpus = 10 }
|
||||
withLabel: highcpu { cpus = 20 }
|
||||
|
||||
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
|
||||
withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
|
||||
withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
|
||||
withLabel: veryhighmem { memory = { get_memory( 75.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)
|
||||
}
|
||||
}
|
||||
12
target/executable/neighbors/find_neighbors/setup_logger.py
Normal file
12
target/executable/neighbors/find_neighbors/setup_logger.py
Normal file
@@ -0,0 +1,12 @@
|
||||
def setup_logger():
|
||||
import logging
|
||||
from sys import stdout
|
||||
|
||||
logger = logging.getLogger()
|
||||
logger.setLevel(logging.INFO)
|
||||
console_handler = logging.StreamHandler(stdout)
|
||||
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
||||
console_handler.setFormatter(logFormatter)
|
||||
logger.addHandler(console_handler)
|
||||
|
||||
return logger
|
||||
Reference in New Issue
Block a user