CI
9a71302308
Build pipeline: openpipelines-bio.openpipeline-spatial.niche-compass-sxfbq
Source commit: 3edcea085b
Source message: merge edits
78 lines
2.0 KiB
YAML
78 lines
2.0 KiB
YAML
name: "from_h5mu_to_spatialexperiment"
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namespace: "convert"
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scope: "public"
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description: |
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Converts an h5mu file into a SpatialExperiment object.
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authors:
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- __merge__: /src/authors/dorien_roosen.yaml
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roles: [ author ]
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arguments:
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- name: "--input"
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alternatives: ["-i"]
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type: file
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description: Input h5mu file
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direction: input
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required: true
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example: input.h5mu
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- name: "--modality"
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type: string
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required: true
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default: "rna"
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description: Name of the modality to be converted.
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- name: "--obsm_spatial_coordinates"
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type: string
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required: false
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description: |
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Key in the .obsm field that contains the spatial coordinates.
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Will be mapped to spatialCoords in the SpatialExperiment object.
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- name: "--output"
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alternatives: ["-o"]
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type: file
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description: Output SpatialExperiment file
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direction: output
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required: true
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example: output.rds
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resources:
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- type: r_script
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path: script.R
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test_resources:
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- type: r_script
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path: test.R
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- path: /resources_test/aviti/aviti_teton_tiny.h5mu
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- path: /resources_test/cosmx/Lung5_Rep2_tiny.h5mu
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- path: /resources_test/xenium/xenium_tiny.h5mu
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engines:
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- type: docker
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image: rocker/r2u:24.04
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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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- type: r
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cran: [ hdf5r, SpatialExperiment ]
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github: scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a
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test_setup:
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- type: docker
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env:
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- RETICULATE_PYTHON=/usr/bin/python
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- PIP_BREAK_SYSTEM_PACKAGES=1
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- type: apt
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packages:
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- python3
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- python3-pip
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- python3-dev
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- python-is-python3
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- libuv1-dev
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- type: r
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cran: [ reticulate, testthat ]
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- type: python
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user: true
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__merge__: /src/base/requirements/anndata_mudata.yaml
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runners:
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- type: executable
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- type: nextflow
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directives:
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label: [lowmem, singlecpu] |