CI
b8ac2db1ac
Build pipeline: openpipelines-bio.openpipeline-qc.build-main-km8q4
Source commit: 31245d83cd
Source message: deploy: 4b5539227ceaa6be5c7e97ca45fcf3aa025466fd
266 lines
7.2 KiB
YAML
266 lines
7.2 KiB
YAML
name: "detect_ingestion_method"
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namespace: "ingestion_qc"
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version: "build_main"
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authors:
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- name: "Dorien Roosen"
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roles:
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- "author"
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info:
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role: "Core Team Member"
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links:
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email: "dorien@data-intuitive.com"
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github: "dorien-er"
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linkedin: "dorien-roosen"
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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 Scientist"
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- name: "Weiwei Schultz"
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roles:
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- "contributor"
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info:
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role: "Contributor"
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organizations:
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- name: "Janssen R&D US"
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role: "Associate Director Data Sciences"
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argument_groups:
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- name: "Inputs"
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arguments:
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- type: "file"
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name: "--input"
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description: "The input h5mu file(s)"
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info: null
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example:
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- "path/to/file.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: "string"
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name: "--modality"
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description: "The modality to use"
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info: null
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default:
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- "rna"
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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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- name: "Outputs"
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arguments:
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- type: "string"
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name: "--output_uns_ingestion_method"
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description: "The .uns field in which to store the exprimental setup. Values stored\
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\ are `cellranger_multi`, `xenium` or `cosmx`."
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info: null
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default:
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- "ingestion_method"
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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: "file"
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name: "--output"
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description: "The output h5mu file, containing an .uns field with experiment description."
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info: null
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example:
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- "path/to/file.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: "output"
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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: "setup_logger.py"
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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: "Detects the ingestion method of a dataset.\nCurrently detects either\
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\ 10X CellRanger Multi, 10X Xenium or Nanostring CosMx, but can be extended to other\
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\ technologies upon request.\n"
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test_resources:
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- type: "python_script"
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path: "test.py"
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is_executable: true
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- type: "file"
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path: "sample_one.qc.h5mu"
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- type: "file"
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path: "Lung5_Rep2_tiny.qc.h5mu"
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- type: "file"
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path: "xenium_tiny.qc.h5mu"
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info: null
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status: "enabled"
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scope:
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image: "public"
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target: "public"
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requirements:
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commands:
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- "ps"
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repositories:
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- type: "github"
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name: "openpipeline"
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repo: "openpipelines-bio/openpipeline"
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tag: "2.1.2"
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- type: "vsh"
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name: "craftbox"
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repo: "craftbox"
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tag: "v0.2.0"
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links:
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repository: "https://github.com/openpipelines-bio/openpipeline_qc"
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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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- "lowdisk"
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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: "python:3.12-slim"
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target_registry: "images.viash-hub.com"
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target_tag: "build_main"
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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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- "procps"
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interactive: false
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- type: "python"
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user: false
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packages:
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- "anndata~=0.11.1"
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- "mudata~=0.3.1"
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script:
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- "exec(\"try:\\n import awkward\\nexcept ModuleNotFoundError:\\n exit(0)\\\
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nelse: exit(1)\")"
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upgrade: true
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test_setup:
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- type: "apt"
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packages:
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- "git"
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interactive: false
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- type: "python"
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user: false
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packages:
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- "viashpy==0.8.0"
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github:
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- "openpipelines-bio/core#subdirectory=packages/python/openpipeline_testutils"
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upgrade: true
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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/ingestion_qc/detect_ingestion_method/config.vsh.yaml"
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runner: "executable"
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engine: "docker|native"
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output: "target/executable/ingestion_qc/detect_ingestion_method"
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executable: "target/executable/ingestion_qc/detect_ingestion_method/detect_ingestion_method"
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viash_version: "0.9.4"
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git_commit: "31245d83cd69ca747cb4610bed18692a3a3914f0"
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git_remote: "https://github.com/openpipelines-bio/openpipeline_qc"
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package_config:
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name: "openpipeline_qc"
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version: "build_main"
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info:
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test_resources:
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- type: "s3"
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path: "s3://openpipelines-bio/openpipeline_incubator/resources_test"
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dest: "resources_test"
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repositories:
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- type: "github"
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name: "openpipeline"
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repo: "openpipelines-bio/openpipeline"
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tag: "2.1.2"
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- type: "vsh"
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name: "craftbox"
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repo: "craftbox"
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tag: "v0.2.0"
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viash_version: "0.9.4"
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source: "src"
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target: "target"
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config_mods:
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- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
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\ := '$id'\n.resources += {path: '/src/configs/labels.config', dest: 'nextflow_labels.config'}\n\
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.runners[.type == 'nextflow'].config.script := 'includeConfig(\"nextflow_labels.config\"\
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)'\n"
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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 := 'build_main'"
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organization: "vsh"
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links:
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repository: "https://github.com/openpipelines-bio/openpipeline_qc"
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docker_registry: "ghcr.io"
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