CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
52 lines
1.5 KiB
Plaintext
52 lines
1.5 KiB
Plaintext
workflow run_wf {
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take:
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input_ch
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main:
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output_ch = input_ch
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// Set aside the output for this workflow to avoid conflicts
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| map {id, state ->
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def new_state = state + ["workflow_output": state.output]
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[id, new_state]
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}
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// cell filtering
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| filter_with_counts.run(
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key: "gdo_filter_with_counts",
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fromState: { id, state ->
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[
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"input": state.input,
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"modality": "gdo",
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"obs_name_filter": "filter_with_counts",
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"var_name_filter": "filter_with_counts",
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"min_counts": state.min_counts,
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"max_counts": state.max_counts,
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"min_genes_per_cell": state.min_guides_per_cell,
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"max_genes_per_cell": state.max_guides_per_cell,
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"min_cells_per_gene": state.min_cells_per_guide,
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"layer": state.layer,
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]
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},
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toState: ["input": "output"]
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)
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| do_filter.run(
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key: "gdo_do_filter",
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fromState : { id, state ->
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// do_filter does not need a layer argument because it filters all layers
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// from a modality.
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def newState = [
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"input": state.input,
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"obs_filter": "filter_with_counts",
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"modality": "gdo",
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"var_filter": "filter_with_counts",
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"output_compression": "gzip",
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"output": state.workflow_output
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]
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return newState
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},
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toState: ["output": "output"],
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auto: [ publish: true ]
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)
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| setState(["output"])
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emit:
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output_ch
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} |