CI
78da099d22
Build pipeline: vsh-ci-build-template-k65s9
Source commit: 532e64485a
Source message: update spatialdata versions
40 lines
1.2 KiB
Plaintext
40 lines
1.2 KiB
Plaintext
nextflow.enable.dsl=2
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include { spatial_qc } from params.rootDir + "/target/nextflow/workflows/qc/spatial_qc/main.nf"
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params.resources_test = params.rootDir + "/resources_test"
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workflow test_wf {
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resources_test = file(params.resources_test)
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output_ch =
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Channel.fromList([
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[
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id: "xenium_test",
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input: resources_test.resolve("xenium/xenium_tiny.h5mu"),
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var_name_mitochondrial_genes: "mitochondrial",
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var_name_ribosomal_genes: "ribosomal",
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]
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])
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| map { state -> [state.id, state] }
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| spatial_qc.run(
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toState: { id, output, state -> output + [og_input: state.input] }
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)
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| view { output ->
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assert output.size() == 2 : "Outputs should contain two elements; [id, state]"
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// check id
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def id = output[0]
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assert id.endsWith("_test")
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// check output
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def state = output[1]
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assert state instanceof Map : "State should be a map. Found: ${state}"
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assert state.containsKey("output") : "Output should contain key 'output'."
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assert state.output.isFile() : "'output' should be a file."
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assert state.output.toString().endsWith(".h5mu") : "Output file should end with '.h5mu'. Found: ${state.output}"
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}
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} |