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Remove some fromState workarounds for older viash versions #943

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merged 1 commit into from
Jan 7, 2025
Merged

Remove some fromState workarounds for older viash versions #943

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40 changes: 12 additions & 28 deletions src/workflows/integration/bbknn_leiden/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,34 +12,18 @@ workflow run_wf {
}
// compute bbknn graph
| bbknn.run(
fromState: { id, state ->
[
input: state.input,
modality: state.modality,
obsm_input: state.obsm_input,
obs_batch: state.obs_batch,
uns_output: state.uns_output,
obsp_distances: state.obsp_distances,
obsp_connectivities: state.obsp_connectivities,
n_neighbors_within_batch: state.n_neighbors_within_batch,
n_pcs: state.n_pcs,
n_trim: state.n_trim
]
},
// use map when viash 0.7.6 is released
// related to https://github.com/viash-io/viash/pull/515
// fromState: [
// "input": "input",
// "obsm_input": "obsm_input",
// "obs_batch": "obs_batch",
// "modality": "modality",
// "uns_output": "uns_output",
// "obsp_distances": "obsp_distances",
// "obsp_connectivities": "obsp_connectivities",
// "n_neighbors_within_batch": "n_neighbors_within_batch",
// "n_pcs": "n_pcs",
// "n_trim": "n_trim"
// ],
fromState: [
"input": "input",
"modality": "modality",
"obsm_input": "obsm_input",
"obs_batch": "obs_batch",
"uns_output": "uns_output",
"obsp_distances": "obsp_distances",
"obsp_connectivities": "obsp_connectivities",
"n_neighbors_within_batch": "n_neighbors_within_batch",
"n_pcs": "n_pcs",
"n_trim": "n_trim",
],
toState: [
"input": "output"
]
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54 changes: 17 additions & 37 deletions src/workflows/integration/scvi_leiden/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,43 +9,23 @@ workflow run_wf {
[id, new_state]
}
| scvi.run(
fromState: {id, state ->
[
"input": state.input,
"obs_batch": state.obs_batch,
"obsm_output": state.obsm_output,
"var_input": state.var_input,
"early_stopping": state.early_stopping,
"early_stopping_monitor": state.early_stopping_monitor,
"early_stopping_patience": state.early_stopping_patience,
"early_stopping_min_delta": state.early_stopping_min_delta,
"max_epochs": state.max_epochs,
"reduce_lr_on_plateau": state.reduce_lr_on_plateau,
"lr_factor": state.lr_factor,
"lr_patience": state.lr_patience,
"output_model": state.output_model,
"modality": state.modality,
"input_layer": state.layer,
]
},
// use map when viash 0.7.6 is released
// related to https://github.com/viash-io/viash/pull/515
// fromState: [
// "input": "input",
// "obs_batch": "obs_batch",
// "obsm_output": "obsm_output",
// "var_input": "var_input",
// "early_stopping": "early_stopping",
// "early_stopping_monitor": "early_stopping_monitor",
// "early_stopping_patience": "early_stopping_patience",
// "early_stopping_min_delta": "early_stopping_min_delta",
// "max_epochs": "max_epochs",
// "reduce_lr_on_plateau": "reduce_lr_on_plateau",
// "lr_factor": "lr_factor",
// "lr_patience": "lr_patience",
// "output_model": "output_model",
// "modality": "modality"
// ],
fromState: [
"input": "input",
"obs_batch": "obs_batch",
"obsm_output": "obsm_output",
"var_input": "var_input",
"early_stopping": "early_stopping",
"early_stopping_monitor": "early_stopping_monitor",
"early_stopping_patience": "early_stopping_patience",
"early_stopping_min_delta": "early_stopping_min_delta",
"max_epochs": "max_epochs",
"reduce_lr_on_plateau": "reduce_lr_on_plateau",
"lr_factor": "lr_factor",
"lr_patience": "lr_patience",
"output_model": "output_model",
"modality": "modality",
"input_layer": "layer",
],
toState: [
"input": "output",
"output_model": "output_model"
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2 changes: 0 additions & 2 deletions src/workflows/qc/qc/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -70,8 +70,6 @@ workflow run_wf {
}
return newState
},
// use map when viash 0.7.6 is released
// related to https://github.com/viash-io/viash/pull/515
toState: ["input": "output"]
)
| publish.run(
Expand Down
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