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Fix argument default and integration tests after #936 (#938)
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DriesSchaumont authored Dec 14, 2024
1 parent b11fb8f commit dfb5754
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -49,7 +49,7 @@

## BUG FIXES

* `scvi_leiden` workflow: fix the input layer argument of the workflow not being passed to the scVI component (PR #936).
* `scvi_leiden` workflow: fix the input layer argument of the workflow not being passed to the scVI component (PR #936 and PR #938).

* `scgpt/embedding`: remove unused argument `dbsn` (PR #875).

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1 change: 0 additions & 1 deletion src/workflows/integration/scvi_leiden/config.vsh.yaml
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Expand Up @@ -20,7 +20,6 @@ argument_groups:
description: Path to the sample.
example: dataset.h5mu
- name: "--layer"
default: "log_normalized"
type: string
description: use specified layer for expression values instead of the .X object from the modality.
required: false
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4 changes: 2 additions & 2 deletions src/workflows/integration/scvi_leiden/test.nf
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Expand Up @@ -12,15 +12,15 @@ workflow test_wf {
[
id: "simple_execution_test",
input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
layer: "log_normalized",
layer: null,
obs_batch: "sample_id",
max_epochs: 1,
output_model: "simple_execution_test_model/"
],
[
id: "no_leiden_resolutions_test",
input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
layer: "log_normalized",
layer: null,
obs_batch: "sample_id",
output_model: "no_leiden_resolutions_test_model/",
max_epochs: 1,
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