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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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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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387
target/executable/annotate/popv/.config.vsh.yaml
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@@ -1,387 +0,0 @@
name: "popv"
namespace: "annotate"
version: "dev"
authors:
- name: "Matthias Beyens"
roles:
- "author"
info:
role: "Contributor"
links:
github: "MatthiasBeyens"
orcid: "0000-0003-3304-0706"
email: "matthias.beyens@gmail.com"
linkedin: "mbeyens"
organizations:
- name: "Janssen Pharmaceuticals"
href: "https://www.janssen.com"
role: "Principal Scientist"
- name: "Robrecht Cannoodt"
roles:
- "author"
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: "Inputs"
description: "Arguments related to the input (aka query) dataset."
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"
description: "Which modality to process."
info: null
default:
- "rna"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--input_layer"
description: "Which layer to use. If no value is provided, the counts are assumed\
\ to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[input_layer]`."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--input_obs_batch"
description: "Key in obs field of input adata for batch information. If no value\
\ is provided, batch label is assumed to be unknown."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--input_var_subset"
description: "Subset the input object with this column."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--input_obs_label"
description: "Key in obs field of input adata for label information. This is only\
\ used for training scANVI. Unlabelled cells should be set to `\"unknown_celltype_label\"\
`."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--unknown_celltype_label"
description: "If `input_obs_label` is specified, cells with this value will be\
\ treated as unknown and will be predicted by the model."
info: null
default:
- "unknown"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Reference"
description: "Arguments related to the reference dataset."
arguments:
- type: "file"
name: "--reference"
description: "User-provided reference tissue. The data that will be used as reference\
\ to call cell types."
info: null
example:
- "TS_Bladder_filtered.h5ad"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--reference_layer"
description: "Which layer to use. If no value is provided, the counts are assumed\
\ to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[reference_layer]`."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--reference_obs_label"
description: "Key in obs field of reference AnnData with cell-type information."
info: null
default:
- "cell_ontology_class"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--reference_obs_batch"
description: "Key in obs field of input adata for batch information."
info: null
default:
- "donor_assay"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
description: "Output arguments."
arguments:
- type: "file"
name: "--output"
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"
info: null
example:
- "gzip"
required: false
choices:
- "gzip"
- "lzf"
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Arguments"
description: "Other arguments."
arguments:
- type: "string"
name: "--methods"
description: "Methods to call cell types. By default, runs to knn_on_scvi and\
\ scanvi."
info: null
example:
- "knn_on_scvi"
- "scanvi"
required: true
choices:
- "celltypist"
- "knn_on_bbknn"
- "knn_on_scanorama"
- "knn_on_scvi"
- "onclass"
- "rf"
- "scanvi"
- "svm"
direction: "input"
multiple: true
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: "Performs popular major vote cell typing on single cell sequence data\
\ using multiple algorithms. Note that this is a one-shot version of PopV."
test_resources:
- type: "python_script"
path: "test.py"
is_executable: true
- type: "file"
path: "annotation_test_data"
- 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:
- "highmem"
- "highcpu"
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:3.9-slim"
target_registry: "images.viash-hub.com"
target_tag: "dev"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "procps"
- "git"
- "build-essential"
- "wget"
interactive: false
- type: "python"
user: false
packages:
- "scanpy~=1.9.6"
- "scvi-tools~=1.0.3"
- "popv~=0.3.2"
- "jax==0.4.10"
- "jaxlib==0.4.10"
- "ml-dtypes<0.3.0"
- "scipy==1.12.0"
upgrade: true
- type: "python"
user: false
packages:
- "anndata==0.10.8"
- "mudata~=0.2.4"
- "pandas!=2.1.2"
- "numpy<2.0.0"
upgrade: true
- type: "docker"
run:
- "cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git && \\\n\
\ cd PopV && git fetch --depth 1 origin tag v0.2 && git checkout v0.2\n"
test_setup:
- type: "python"
user: false
packages:
- "viashpy==0.8.0"
upgrade: true
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/annotate/popv/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/annotate/popv"
executable: "target/executable/annotate/popv/popv"
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"