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Remove grouping bottleneck #42

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merged 3 commits into from
Jan 21, 2025
Merged

Remove grouping bottleneck #42

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b2bd8ae
Add groupKey to clustering grouping
lazappi Jan 21, 2025
e0ece7b
Remove unused clustering arguments from benchmark
lazappi Jan 21, 2025
ced624f
Restore resolutions argument to benchmark workflow
lazappi Jan 21, 2025
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9 changes: 6 additions & 3 deletions src/data_processors/process_integration/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -44,9 +44,12 @@ workflow run_wf {

// group by original dataset id
| map{id, state ->
[state.prevId, state]
// groupKey() allows us to set a size for each group based on the state
// which means each group can continue once it is complete
[groupKey(state.prevId, state.resolutions.size()), state]
}
| groupTuple()
// Group and sort by resolution to ensure the order is consistent
| groupTuple(sort: { res1, res2 -> res1.resolution <=> res2.resolution })

// merge the clustering results into one state
| map{ id, states ->
Expand All @@ -60,7 +63,7 @@ workflow run_wf {
def clusterings = states.collect { it.output_clustering }
def newState = states[0] + ["clusterings": clusterings]

[id, newState]
[id.toString(), newState]
}

// merge clustering results into dataset h5ad
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3 changes: 2 additions & 1 deletion src/workflows/run_benchmark/main.nf
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Expand Up @@ -148,7 +148,8 @@ workflow run_wf {
fromState: [
input_integrated: "method_output",
input_dataset: "input_dataset",
expected_method_types: "method_types"
expected_method_types: "method_types",
resolutions: "resolutions"
],
toState: { id, output, state ->
// Add method types to the state
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