diff --git a/src/workflows/integration/bbknn_leiden/main.nf b/src/workflows/integration/bbknn_leiden/main.nf index 97a518129af..474d12ff770 100644 --- a/src/workflows/integration/bbknn_leiden/main.nf +++ b/src/workflows/integration/bbknn_leiden/main.nf @@ -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" ] diff --git a/src/workflows/integration/scvi_leiden/main.nf b/src/workflows/integration/scvi_leiden/main.nf index 185e02ac42a..ac418ee4f7e 100644 --- a/src/workflows/integration/scvi_leiden/main.nf +++ b/src/workflows/integration/scvi_leiden/main.nf @@ -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" diff --git a/src/workflows/qc/qc/main.nf b/src/workflows/qc/qc/main.nf index fa22f332263..650170e08ff 100644 --- a/src/workflows/qc/qc/main.nf +++ b/src/workflows/qc/qc/main.nf @@ -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(