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Build branch fix-integration-tests with version fix-integration-tests (c1fe2a62)

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Build pipeline: vsh-ci-dev-rdkgl

Source commit: c1fe2a629d

Source message: Update CHANGELOG
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CI
2024-10-18 08:08:08 +00:00
parent cd0af18851
commit 43cfb251c7
1457 changed files with 222 additions and 905786 deletions
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347
target/executable/dimred/tsne/.config.vsh.yaml
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@@ -1,347 +0,0 @@
name: "tsne"
namespace: "dimred"
version: "dev"
authors:
- name: "Jakub Majercik"
roles:
- "maintainer"
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: "--input"
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: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--use_rep"
description: "The `.obsm` slot to use as input for the tSNE computation."
info: null
example:
- "X_pca"
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Output h5mu file."
info: null
example:
- "output.h5mu"
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:
- "gzip"
required: false
choices:
- "gzip"
- "lzf"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--obsm_output"
description: "The .obsm key to use for storing the tSNE results."
info: null
default:
- "X_tsne"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Arguments"
arguments:
- type: "integer"
name: "--n_pcs"
description: "The number of principal components to use for the tSNE computation."
info: null
default:
- 50
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--perplexity"
description: "The perplexity is related to the number of nearest neighbors that\
\ is used in other manifold learning algorithms. Larger datasets usually require\
\ a larger perplexity. Consider selecting a value between 5 and 50. Different\
\ values can result in significantly different results."
info: null
default:
- 30.0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--min_dist"
description: "The effective minimum distance between embedded points. Smaller\
\ values will result in a more clustered/clumped embedding where nearby points\
\ on the manifold are drawn closer together, while larger values will result\
\ on a more even dispersal of points. The value should be set relative to the\
\ spread value, which determines the scale at which embedded points will be\
\ spread out."
info: null
default:
- 0.5
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--metric"
description: "Distance metric to calculate neighbors on."
info: null
default:
- "euclidean"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--early_exaggeration"
description: "Controls how tight natural clusters in the original space are in\
\ the embedded space and how much space will be between them. For larger values,\
\ the space between natural clusters will be larger in the embedded space. Again,\
\ the choice of this parameter is not very critical. If the cost function increases\
\ during initial optimization, the early exaggeration factor or the learning\
\ rate might be too high."
info: null
default:
- 12.0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "double"
name: "--learning_rate"
description: "The learning rate for t-SNE optimization. Typical values range between\
\ 10.0 and 1000.0."
info: null
default:
- 1000.0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--random_state"
description: "The random seed to use for the tSNE computation."
info: null
default:
- 0
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: "t-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality\
\ reduction technique used to visualize high-dimensional data in a low-dimensional\
\ space, revealing patterns and clusters by preserving local data similarities.\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:
- "highcpu"
- "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: "dev"
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/dimred/tsne/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/dimred/tsne"
executable: "target/executable/dimred/tsne/tsne"
viash_version: "0.9.0"
git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
git_tag: "0.2.0-1926-g2dbe3b72"
package_config:
name: "openpipeline"
version: "dev"
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\")'"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'dev'"
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"