Build branch fix-integration-tests with version fix-integration-tests (c1fe2a62)
Build pipeline: vsh-ci-dev-rdkgl
Source commit: c1fe2a629d
Source message: Update CHANGELOG
This commit is contained in:
@@ -1,216 +0,0 @@
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name: "from_h5mu_to_seurat"
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namespace: "convert"
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version: "dev"
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authors:
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- name: "Robrecht Cannoodt"
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roles:
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- "author"
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- "maintainer"
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info:
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role: "Core Team Member"
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links:
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email: "robrecht@data-intuitive.com"
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github: "rcannood"
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orcid: "0000-0003-3641-729X"
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linkedin: "robrechtcannoodt"
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organizations:
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- name: "Data Intuitive"
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href: "https://www.data-intuitive.com"
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role: "Data Science Engineer"
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- name: "Open Problems"
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href: "https://openproblems.bio"
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role: "Core Member"
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argument_groups:
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- name: "Arguments"
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arguments:
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- type: "file"
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name: "--input"
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alternatives:
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- "-i"
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description: "Input h5mu file"
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info: null
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example:
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- "input.h5mu"
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must_exist: true
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create_parent: true
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required: true
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direction: "input"
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multiple: false
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multiple_sep: ";"
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- type: "file"
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name: "--output"
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alternatives:
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- "-o"
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description: "Output Seurat file"
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info: null
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example:
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- "output.rds"
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must_exist: true
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create_parent: true
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required: true
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direction: "output"
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multiple: false
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multiple_sep: ";"
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resources:
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- type: "r_script"
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path: "script.R"
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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: "Converts an h5mu file into a Seurat file.\n\nRestrictions:\n - Only\
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\ the intersection of cells is currently loaded into the Seurat object due to the\
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\ object structure limitation.\n - Multimodal embeddings (global .obsm slot) are\
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\ loaded with the assay.used field set to the default assay.\n - Embeddings names\
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\ are changed in order to comply with R & Seurat requirements and conventions.\n\
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\ - Feature names with underscores ('_') are automatically replaced with dashes\
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\ ('-')\n - Seurat does not support global variables metadata /var.\n"
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test_resources:
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- type: "r_script"
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path: "run_test.R"
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is_executable: true
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- type: "file"
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path: "10x_5k_anticmv"
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- type: "file"
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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"
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- type: "nextflow"
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id: "nextflow"
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directives:
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label:
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- "lowmem"
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- "singlecpu"
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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
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publish: false
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config:
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labels:
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mem1gb: "memory = 1000000000.B"
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mem2gb: "memory = 2000000000.B"
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mem5gb: "memory = 5000000000.B"
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mem10gb: "memory = 10000000000.B"
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mem20gb: "memory = 20000000000.B"
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mem50gb: "memory = 50000000000.B"
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mem100gb: "memory = 100000000000.B"
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mem200gb: "memory = 200000000000.B"
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mem500gb: "memory = 500000000000.B"
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mem1tb: "memory = 1000000000000.B"
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mem2tb: "memory = 2000000000000.B"
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mem5tb: "memory = 5000000000000.B"
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mem10tb: "memory = 10000000000000.B"
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mem20tb: "memory = 20000000000000.B"
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mem50tb: "memory = 50000000000000.B"
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mem100tb: "memory = 100000000000000.B"
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mem200tb: "memory = 200000000000000.B"
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mem500tb: "memory = 500000000000000.B"
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mem1gib: "memory = 1073741824.B"
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mem2gib: "memory = 2147483648.B"
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mem4gib: "memory = 4294967296.B"
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mem8gib: "memory = 8589934592.B"
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mem16gib: "memory = 17179869184.B"
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mem32gib: "memory = 34359738368.B"
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mem64gib: "memory = 68719476736.B"
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mem128gib: "memory = 137438953472.B"
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mem256gib: "memory = 274877906944.B"
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mem512gib: "memory = 549755813888.B"
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mem1tib: "memory = 1099511627776.B"
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mem2tib: "memory = 2199023255552.B"
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mem4tib: "memory = 4398046511104.B"
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mem8tib: "memory = 8796093022208.B"
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mem16tib: "memory = 17592186044416.B"
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mem32tib: "memory = 35184372088832.B"
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mem64tib: "memory = 70368744177664.B"
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mem128tib: "memory = 140737488355328.B"
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mem256tib: "memory = 281474976710656.B"
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mem512tib: "memory = 562949953421312.B"
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cpu1: "cpus = 1"
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cpu2: "cpus = 2"
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cpu5: "cpus = 5"
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cpu10: "cpus = 10"
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cpu20: "cpus = 20"
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cpu50: "cpus = 50"
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cpu100: "cpus = 100"
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cpu200: "cpus = 200"
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cpu500: "cpus = 500"
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cpu1000: "cpus = 1000"
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script:
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- "includeConfig(\"nextflow_labels.config\")"
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debug: false
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container: "docker"
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engines:
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- type: "docker"
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id: "docker"
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image: "rocker/r2u:24.04"
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target_registry: "images.viash-hub.com"
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target_tag: "dev"
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namespace_separator: "/"
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setup:
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- type: "apt"
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packages:
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- "libhdf5-dev"
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- "libgeos-dev"
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interactive: false
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- type: "r"
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cran:
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- "anndata"
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- "hdf5r"
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- "testthat"
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- "SeuratObject"
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- "Seurat"
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bioc_force_install: false
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- type: "r"
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github:
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- "pmbio/MuDataSeurat@empty-tables-and-nullable"
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bioc_force_install: false
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entrypoint: []
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cmd: null
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- type: "native"
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id: "native"
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build_info:
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config: "src/convert/from_h5mu_to_seurat/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/convert/from_h5mu_to_seurat"
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executable: "target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat"
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viash_version: "0.9.0"
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git_commit: "2dbe3b7231f9abb4baa628e76e8abc686e627087"
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git_remote: "https://x-access-token:ghs_NVsRTpmVPn6SfFQ131njHQOgn6tt7b1bmmJj@github.com/openpipelines-bio/openpipeline"
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git_tag: "0.2.0-1926-g2dbe3b72"
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package_config:
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name: "openpipeline"
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version: "dev"
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info:
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test_resources:
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- type: "s3"
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path: "s3://openpipelines-data"
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dest: "resources_test"
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viash_version: "0.9.0"
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source: "src"
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target: "target"
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config_mods:
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- ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
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.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
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.runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
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\ := 'includeConfig(\"nextflow_labels.config\")'"
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- ".engines += { type: \"native\" }"
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- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
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- ".engines[.type == 'docker'].target_tag := 'dev'"
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organization: "vsh"
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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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homepage: "https://openpipelines.bio"
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documentation: "https://openpipelines.bio/fundamentals"
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issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"
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