Build branch fix-integration-tests with version fix-integration-tests (da62b4ff)

Build pipeline: vsh-ci-dev-gckj5

Source commit: da62b4ffe3

Source message: Add labels to qc_test component

CHANGELOG.md

@@ -1,4 +1,4 @@
-# openpipelines x.x.x
+# openpipelines 2.x.x (Unreleased)
 
 ## BREAKING CHANGES
 
@@ -42,8 +42,6 @@
   - Store label probabilities instead of uncertainties
   - Take `.h5mu` format as an input instead of `.h5ad`
 
-* `labels_transfer/knn`: delete outdated component due to its functionality now implemented in `labels_transfer/pynndescent_knn`
-
 * `reference/build_cellranger_arc_reference`: a default value of "output" is now specified for the argument `--genome`, inline with `reference/build_cellranger_reference` component. Additionally, providing a value for `--organism` is no longer required and its default value of `Homo Sapiens` has been removed (PR #864).
 
 ## NEW FUNCTIONALITY
@@ -91,8 +89,6 @@
 
 * `dataflow/split_h5mu` component: Added a component to split a single h5mu file into multiple h5mu files based on the values of an .obs column (PR #824).
 
-* `labels_transfer/pynndescent_knn`: component: Added a component for KNN classification based on a PyNNDescent neighborhood graph (PR #830).
-
 * `workflows/test_workflows/ingestion` components & `workflows/ingestion`: Added standalone components for integration testing of ingestion workflows (PR #801). 
 
 * `workflows/ingestion/make_reference`: Add additional arguments passed through to the STAR and BD Rhapsody reference components (PR #846).
@@ -103,7 +99,7 @@
 
 * `dimred/densmap` component: Added a densMAP dimensionality reduction component (PR #748).
 
-* `annotete/scanvi` component: Added a component to annotate cells using scANVI (PR #833).
+* `annotate/scanvi` component: Added a component to annotate cells using scANVI (PR #833).
 
 * `transform/bpcells_regress_out` component: Added a component to regress out effects of confounding variables in the count matrix using BPCells (PR #863).
 
@@ -129,6 +125,10 @@
 
 * `metadata/duplicate_var` component: Added a component to make a copy from one .var field or index to another .var field within the same MuData object (PR #877).
 
+* `filter/subset_obsp` component: Added a component to subset an .obsp matrix by column based on the value of an .obs field. The resulting subset is moved to an .obsm field (PR #888).
+
+* `labels_transfer/knn` component: Enable using additional distance functions for KNN classification (PR #830) and allow to perform KNN classification based on a pre-calculated neighborhood graph (PR #890).
+
 ## MINOR CHANGES
 
 * `resources_test_scripts/cellranger_atac_tiny_bcl.sh` script: generate counts from fastq files using CellRanger atac count (PR #726).
@@ -142,8 +142,6 @@
 
 * Bump scvelo to `0.3.2` (PR #828).
 
-* Bump viash to `0.8.6` (PR #815).
-
 * Pin numpy<2 for several components (PR #815).
 
 * Added `resources_test_scripts/cellranger_atac_tiny_bcl.sh` script: download tiny bcl file with an ATAC experiment, download a motifs file, demultiplex bcl files to reads in fastq format (PR #726).
@@ -162,23 +160,38 @@
 
 ## BUG FIXES
 
-* `dataflow/concatenate_h5mu`: fix writing out multidimensional annotation dataframes (e.g. `.varm`) that had their 
-  data dtype (dtype) changed as a result of adding more observations after concatenation, causing `TypeError`.
-  One notable example of this happening is when one of the samples does not have a multimodal annotation dataframe 
-  which is present in another sample; causing the values being filled with `NA` (PR #837).
-
-* `qc/calculate_qc_metrics`: increase total counts accuracy with low precision floating dtypes as input layer (PR #852).
-
 * Fix failing tests for `ingestion/cellranger_postprocessing`, `ingestion/conversion` and `multiomics/process_batches` (PR #869).
 
 * `convert/from_10xh5_to_h5mu`: add .uns slot to mdata root when metrics file is provided (PR #887).
 
 * Use `params.resources_test` in test workflows in order to point to an alternative location (e.g. a cache).
+* Fix ingestion components not working when optional arguments are unset (PR #894).
 
 ## DOCUMENTATION
 
 * Update authorship of components (PR #835).
 
+# openpipelines 1.0.3
+
+## BUG FIXES
+
+* `qc/calculate_qc_metrics`: increase total counts accuracy with low precision floating dtypes as input layer (PR # , backported from PR #852).
+
+# openpipelines 1.0.2
+
+## BUG FIXES
+
+* `dataflow/concatenate_h5mu`: fix writing out multidimensional annotation dataframes (e.g. `.varm`) that had their 
+  data dtype (dtype) changed as a result of adding more observations after concatenation, causing `TypeError`.
+  One notable example of this happening is when one of the samples does not have a multimodal annotation dataframe 
+  which is present in another sample; causing the values being filled with `NA` (PR #842, backported from PR #837).
+
+# openpipelines 1.0.1
+
+## BUG FIXES
+
+* Bump viash to `0.8.6` (PR #816, backported from #815). This changes the at-runtime generated nextflow process from an in-memory to an on-disk temporary file, which should cause less issues with Nextflow Fusion.
+
 # openpipelines 1.0.0-rc6
 
 ## BUG FIXES

src/annotate/scanvi/config.vsh.yaml

@@ -23,27 +23,26 @@ argument_groups:
         type: string
         default: "rna"
         required: false
+      - name: "--var_input_gene_names"
+        description: .var field containing the gene names, if the .var index is not to be used.
+        type: string
+        required: false
 
-  - name: Reference
-    description: Arguments related to the reference dataset.
+  - name: Reference model
+    description: Arguments related to the reference model.
     arguments:
-      - name: "--reference"
-        type: file
-        description: Reference h5mu file.
-        direction: input
-        required: true
-        example: reference.h5mu
       - name: "--scvi_reference_model"
         type: file
-        description: "Pretrained scvi reference model"
+        description: "Pretrained SCVI reference model to initialize the SCANVI model with. The model needs to include the AnnData object used to trained the model stored. "
         example: scvi_model.pt
         direction: input
-        required: true
-      - name: "--reference_obs_label"
-        type: string
-        description: Key in obs field of reference AnnData with cell-type information.
-        example: "cell_ontology_class"
-        required: true
+        required: false
+      - name: "--scanvi_reference_model"
+        type: file
+        description: "Pretrained SCANVI reference model."
+        example: scvi_model.pt
+        direction: input
+        required: false
 
   - name: SCANVI reference model training arguments
     description: Arguments related to the reference SCANVI model.
@@ -190,6 +189,7 @@ resources:
   - type: python_script
     path: script.py
   - path: /src/utils/setup_logger.py
+  - path: /src/annotate/utils/query_reference_allignment.py
 
 test_resources:
   - type: python_script

src/annotate/scanvi/script.py

@@ -7,14 +7,39 @@ import numpy as np
 par = {
     "input": "resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu",
     "modality": "rna",
-    "reference": "resources_test/annotation_test_data/TS_Blood_filtered.h5ad",
-    "scvi_reference_model": "resources_test/annotation_test_data/scvi_model.pt",
-    "reference_obs_label": "cell_ontology_class",
+    "var_query_gene_names": None,
+    "scvi_reference_model": "resources_test/annotation_test_data/scvi_model",
+    "scanvi_reference_model": None,
+    "unknown_celltype": "Unkown",
+    "output": "output.h5mu",
+    "output_obsm_scanvi_embedding": "scanvi_embedding",
+    "output_obs_predictions": "scanvi_pred",
+    "output_obs_probability": "scanvi_probability",
+    "output_model": None,
+    "output_compression": None,
+    "reference_learning_rate": 1e-3,
+    "reference_reduce_lr_on_plateau": True,
+    "reference_lr_patience": 25,
+    "reference_lr_factor": 0.5,
+    "reference_train_size": 0.9,
+    "reference_max_epochs": 10,
+    "reference_early_stopping": True,
+    "reference_early_stopping_patience": 50,
+    "query_train_size": 0.9,
+    "query_max_epochs": 10,
+    "query_learning_rate": 1e-3,
+    "query_reduce_lr_on_plateau": True,
+    "query_lr_patience": 25,
+    "query_lr_factor": 0.5,
+    "query_early_stopping": True,
+    "query_early_stopping_patience": 50
 }
-meta = {}
+meta = {"resources_dir": "src/annotate/utils"}
 ## VIASH END
 
 sys.path.append(meta["resources_dir"])
+from query_reference_allignment import set_var_index, cross_check_genes
+
 # START TEMPORARY WORKAROUND setup_logger
 # reason: resources aren't available when using Nextflow fusion
 # from setup_logger import setup_logger
@@ -33,72 +58,104 @@ def setup_logger():
 # END TEMPORARY WORKAROUND setup_logger
 logger = setup_logger()
 
-logger.info("Reading the input and reference data")
+if (not par["scvi_reference_model"]) and not (par["scanvi_reference_model"]) or (par["scvi_reference_model"] and par["scanvi_reference_model"]):
+    raise ValueError("Make sure to provide either an '--scvi_reference_model' or a '--scanvi_reference_model', but not both.")
 
-input_data = mu.read_h5mu(par["input"])
-query = input_data.mod[par["modality"]]
-reference_data = mu.read_h5mu(par["reference"])
-reference = reference_data.mod[par["modality"]]
 
-logger.info(f"Loading the pretrained scVI model from {par['scvi_reference_model']}")
-scvi_reference_model = scvi.model.SCVI.load(par["scvi_reference_model"], reference)
+def main():
+    logger.info("Reading the query data")
+    # Read in data
+    input_data = mu.read_h5mu(par["input"])
+    input_modality = input_data.mod[par["modality"]].copy()
+    # scANVI requires query and reference gene names to be equivalent 
+    input_modality = set_var_index(input_modality, par["var_input_gene_names"])
 
-logger.info("Setting up scANVI model")
+    if par["scanvi_reference_model"]:
 
-scanvi_ref = scvi.model.SCANVI.from_scvi_model(
-    scvi_reference_model,
-    unlabeled_category=par["unknown_celltype"],
-    labels_key=par["reference_obs_label"],
+        logger.info(f"Loading the pretrained scANVI model from {par['scanvi_reference_model']} and updating it with the query data {par['input']}")
+        scanvi_query = scvi.model.SCANVI.load_query_data(
+            input_modality,
+            par["scanvi_reference_model"],
+            freeze_classifier=True,
+            inplace_subset_query_vars=True
+            )
+
+    elif par["scvi_reference_model"]:
+
+        logger.info("Reading in the reference model and associated reference data")
+        scvi_reference_model = scvi.model.SCVI.load(par["scvi_reference_model"])
+        reference = scvi_reference_model.adata
+
+
+        logger.info("Alligning genes in reference and query dataset")
+        # scANVI requires query and reference gene names to be equivalent 
+        reference = set_var_index(reference)
+        # Subset query dataset based on genes present in reference
+        common_ens_ids = cross_check_genes(input_modality, reference)
+        input_modality = input_modality[:, common_ens_ids]
+
+        logger.info("Instantiating scANVI model from the scVI model")
+        scanvi_ref = scvi.model.SCANVI.from_scvi_model(
+            scvi_reference_model,
+            unlabeled_category=par["unknown_celltype"],
+            labels_key=scvi_reference_model.adata_manager._registry["setup_args"]["labels_key"],
+            )
+
+        reference_plan_kwargs = {
+            "lr": par["reference_learning_rate"],
+            "reduce_lr_on_plateau": par['reference_reduce_lr_on_plateau'],
+            "lr_patience": par['reference_lr_patience'],
+            "lr_factor": par['reference_lr_factor']
+            }
+
+        logger.info("Training scANVI model on reference data with celltype labels")
+
+        scanvi_ref.train(
+            train_size=par["reference_train_size"],
+            max_epochs=par['reference_max_epochs'],
+            early_stopping=par['reference_early_stopping'],
+            early_stopping_patience=par['reference_early_stopping_patience'],
+            plan_kwargs=reference_plan_kwargs,
+            check_val_every_n_epoch=1,
+            accelerator="auto"
+        )
+
+        logger.info(f"Updating scANVI model with query data {par['input']}")
+        scvi.model.SCANVI.prepare_query_anndata(input_modality, scanvi_ref, inplace=True)
+        scanvi_query = scvi.model.SCANVI.load_query_data(input_modality, scanvi_ref)
+
+    logger.info("Training scANVI model with query data")
+    query_plan_kwargs = {
+        "lr": par["query_learning_rate"],
+        "reduce_lr_on_plateau": par['query_reduce_lr_on_plateau'],
+        "lr_patience": par['query_lr_patience'],
+        "lr_factor": par['query_lr_factor']
+        }
+
+    scanvi_query.train(
+        train_size=par["query_train_size"],
+        max_epochs=par['query_max_epochs'],
+        early_stopping=par['query_early_stopping'],
+        early_stopping_patience=par['query_early_stopping_patience'],
+        plan_kwargs=query_plan_kwargs,
+        check_val_every_n_epoch=1,
+        accelerator="auto"
     )
 
-reference_plan_kwargs = {"lr": par["reference_learning_rate"],
-                         "reduce_lr_on_plateau": par['reference_reduce_lr_on_plateau'],
-                         "lr_patience": par['reference_lr_patience'],
-                         "lr_factor": par['reference_lr_factor']
-                        }
+    logger.info("Adding latent representation to query data")
+    input_modality.obsm[par["output_obsm_scanvi_embedding"]] = scanvi_query.get_latent_representation()
 
-logger.info("Training scANVI model on reference data with celltype labels")
+    logger.info("Running predictions on query data")
+    input_modality.obs[par["output_obs_predictions"]] = scanvi_query.predict(input_modality)
+    input_modality.obs[par["output_obs_probability"]] = np.max(scanvi_query.predict(input_modality, soft=True), axis=1)
 
-scanvi_ref.train(
-    train_size=par["reference_train_size"],
-    max_epochs=par['reference_max_epochs'],
-    early_stopping=par['reference_early_stopping'],
-    early_stopping_patience=par['reference_early_stopping_patience'],
-    plan_kwargs=reference_plan_kwargs,
-    check_val_every_n_epoch=1,
-    accelerator="auto",
-)
+    logger.info("Saving output and model")
+    input_data.mod[par["modality"]] = input_modality
+    input_data.write_h5mu(par["output"], compression=par["output_compression"])
 
-logger.info("Updating and training scANVI model with query data")
-scvi.model.SCANVI.prepare_query_anndata(query, scanvi_ref, inplace=True)
-scanvi_query = scvi.model.SCANVI.load_query_data(query, scanvi_ref)
+    if par["output_model"]:
+        scanvi_query.save(par["output_model"], overwrite=True)
 
-query_plan_kwargs = {"lr": par["query_learning_rate"],
-                     "reduce_lr_on_plateau": par['query_reduce_lr_on_plateau'],
-                     "lr_patience": par['query_lr_patience'],
-                     "lr_factor": par['query_lr_factor']
-                    }
 
-scanvi_query.train(
-    train_size=par["query_train_size"],
-    max_epochs=par['query_max_epochs'],
-    early_stopping=par['query_early_stopping'],
-    early_stopping_patience=par['query_early_stopping_patience'],
-    plan_kwargs=query_plan_kwargs,
-    check_val_every_n_epoch=1,
-    accelerator="auto",
-)
-
-logger.info("Adding latent representation to query data")
-query.obsm[par["output_obsm_scanvi_embedding"]] = scanvi_query.get_latent_representation()
-
-logger.info("Running predictions on query data")
-query.obs[par["output_obs_predictions"]] = scanvi_query.predict(query)
-query.obs[par["output_obs_probability"]] = np.max(scanvi_query.predict(query, soft=True), axis=1)
-
-logger.info("Saving output and model")
-input_data.mod[par["modality"]] = query
-input_data.write_h5mu(par["output"], compression=par["output_compression"])
-
-if par["output_model"]:
-    scanvi_query.save(par["output_model"], overwrite=True)
+if __name__ == '__main__':
+    main()

src/annotate/scanvi/test.py

@@ -1,9 +1,9 @@
+import subprocess
 import sys
 import os
 import pytest
 import re
 import mudata as mu
-import anndata as ad
 from openpipelinetestutils.asserters import assert_annotation_objects_equal
 import scvi
 import os
@@ -16,6 +16,7 @@ meta = {
 input_file = f"{meta['resources_dir']}/pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"
 reference_file = f"{meta['resources_dir']}/annotation_test_data/TS_Blood_filtered.h5mu"
 
+
 @pytest.fixture
 def create_scvi_model(random_path, tmp_path):
     def wrapper(input_file, reference_file):
@@ -23,7 +24,7 @@ def create_scvi_model(random_path, tmp_path):
         input_modality = input_data.mod["rna"]
         reference_data = mu.read_h5mu(reference_file)
         reference_modality = reference_data.mod["rna"]
-        
+
         reference_data.var["gene_symbol"] = list(reference_data.var.index)
         reference_data.var.index = [re.sub("\\.[0-9]+$", "", s) for s in reference_data.var["ensemblid"]]
         reference_modality.var["gene_symbol"] = list(reference_modality.var.index)
@@ -47,30 +48,49 @@ def create_scvi_model(random_path, tmp_path):
             n_layers=1,
             )
         scvi_model.train(max_epochs=10)
-        
+
         input_data.mod["rna"] = query
-        reference_data.mod["rna"] = reference
-        
+        # reference_data.mod["rna"] = reference
+
         input_data_file = random_path(extension="h5mu")
-        reference_file = random_path(extension="h5mu")
+        # reference_file = random_path(extension="h5mu")
         scvi_model_file = tmp_path
-        
+
         input_data.write_h5mu(input_data_file)
-        reference_data.write_h5mu(reference_file)
-        scvi_model.save(scvi_model_file, overwrite=True)
-                
-        return scvi_model_file, input_data_file, reference_file
+        # reference_data.write_h5mu(reference_file)
+        scvi_model.save(scvi_model_file, save_anndata=True, overwrite=True)
+
+        return scvi_model_file, input_data_file
     return wrapper
 
+
+@pytest.fixture
+def create_scanvi_model(create_scvi_model, tmp_path):
+    def scanvi_wrapper():
+        scvi_model_file, input_data_file = create_scvi_model(input_file, reference_file)
+
+        scvi_model = scvi.model.SCVI.load(scvi_model_file)
+        scanvi_model = scvi.model.SCANVI.from_scvi_model(
+            scvi_model,
+            unlabeled_category="Unkown",
+            labels_key="cell_ontology_class",
+            )
+        scanvi_model.train(max_epochs=10)
+
+        scanvi_model_file = tmp_path
+        scanvi_model.save(scanvi_model_file, save_anndata=True, overwrite=True)
+
+        return scanvi_model_file, input_data_file
+    return scanvi_wrapper
+
+
 def test_simple_execution(run_component, random_h5mu_path, create_scvi_model):
-    scvi_model_file, input_file_scvi, reference_file_scvi = create_scvi_model(input_file, reference_file)
+    scvi_model_file, input_file_scvi = create_scvi_model(input_file, reference_file)
     output_file = random_h5mu_path()
 
     run_component([
         "--input", input_file_scvi,
-        "--reference", reference_file_scvi,
         "--scvi_reference_model", scvi_model_file,
-        "--reference_obs_label", "cell_ontology_class",
         "--reference_max_epochs", "10",
         "--query_max_epochs", "10",
         "--output", output_file
@@ -80,7 +100,7 @@ def test_simple_execution(run_component, random_h5mu_path, create_scvi_model):
 
     input_mudata = mu.read_h5mu(input_file_scvi)
     output_mudata = mu.read_h5mu(output_file)
-    
+
     assert input_mudata.mod["rna"].n_obs == output_mudata.mod["rna"].n_obs, f"Number of observations changed"
     assert input_mudata.mod["rna"].n_vars == output_mudata.mod["rna"].n_vars, f"Number of variables changed"
     assert "scanvi_embedding" in output_mudata.mod["rna"].obsm.keys(), "Latent representation not added"
@@ -89,16 +109,15 @@ def test_simple_execution(run_component, random_h5mu_path, create_scvi_model):
 
     assert_annotation_objects_equal(input_mudata.mod["prot"],
                                     output_mudata.mod["prot"])
-    
+
+
 def test_multiple_arguments(run_component, random_h5mu_path, create_scvi_model, tmp_path):
-    scvi_model_file, input_file_scvi, reference_file_scvi = create_scvi_model(input_file, reference_file)
+    scvi_model_file, input_file_scvi = create_scvi_model(input_file, reference_file)
     output_file = random_h5mu_path()
 
     run_component([
         "--input", input_file_scvi,
-        "--reference", reference_file_scvi,
         "--scvi_reference_model", scvi_model_file,
-        "--reference_obs_label", "cell_ontology_class",
         "--output", output_file,
         "--reference_max_epochs", "10",
         "--reference_reduce_lr_on_plateau", "True",
@@ -123,20 +142,69 @@ def test_multiple_arguments(run_component, random_h5mu_path, create_scvi_model,
     ])
 
     assert os.path.exists(output_file), "Output file does not exist"
-    assert os.path.exists(tmp_path / "model.pt"), "Model file does not exist" 
+    assert os.path.exists(tmp_path / "model.pt"), "Model file does not exist"
 
     input_mudata = mu.read_h5mu(input_file_scvi)
     output_mudata = mu.read_h5mu(output_file)
-    
+
     assert input_mudata.mod["rna"].n_obs == output_mudata.mod["rna"].n_obs, f"Number of observations changed"
     assert input_mudata.mod["rna"].n_vars == output_mudata.mod["rna"].n_vars, f"Number of variables changed"
     assert "scanvi_embedding" in output_mudata.mod["rna"].obsm.keys(), "Latent representation not added"
     assert "scanvi_pred" in output_mudata.mod["rna"].obs.keys(), "Predictions not added"
     assert "scanvi_probability" in output_mudata.mod["rna"].obs.keys(), "Probabilities not added"
 
+    assert_annotation_objects_equal(input_mudata.mod["prot"],
+                                    output_mudata.mod["prot"])
+
+
+def test_pretrained_scanvi(run_component, random_h5mu_path, create_scanvi_model):
+    scanvi_model_file, input_file_scanvi = create_scanvi_model()
+    output_file = random_h5mu_path()
+
+    run_component([
+        "--input", input_file_scanvi,
+        "--scanvi_reference_model", scanvi_model_file,
+        "--reference_obs_label", "cell_ontology_class",
+        "--reference_max_epochs", "10",
+        "--query_max_epochs", "10",
+        "--output", output_file
+    ])
+
+    assert os.path.exists(output_file), "Output file does not exist"
+
+    input_mudata = mu.read_h5mu(input_file_scanvi)
+    output_mudata = mu.read_h5mu(output_file)
+
+    assert input_mudata.mod["rna"].n_obs == output_mudata.mod["rna"].n_obs, f"Number of observations changed"
+    assert input_mudata.mod["rna"].n_vars == output_mudata.mod["rna"].n_vars, f"Number of variables changed"
+    assert "scanvi_embedding" in output_mudata.mod["rna"].obsm.keys(), "Latent representation not added"
+    assert "scanvi_pred" in output_mudata.mod["rna"].obs.keys(), "Predictions not added"
+    assert "scanvi_probability" in output_mudata.mod["rna"].obs.keys(), "Probabilities not added"
 
     assert_annotation_objects_equal(input_mudata.mod["prot"],
                                     output_mudata.mod["prot"])
 
+
+def test_raises(run_component, random_h5mu_path, create_scvi_model, create_scanvi_model):
+    scvi_model_file, input_file_scvi = create_scvi_model(input_file, reference_file)
+    scanvi_model_file, input_file_scanvi = create_scanvi_model()
+    output_file = random_h5mu_path()
+
+    with pytest.raises(subprocess.CalledProcessError) as err:
+        run_component([
+            "--input", input_file_scanvi,
+            "--scanvi_reference_model", scanvi_model_file,
+            "--scvi_reference_model", scvi_model_file,
+            "--reference_obs_label", "cell_ontology_class",
+            "--reference_max_epochs", "10",
+            "--query_max_epochs", "10",
+            "--output", output_file
+        ])
+    assert re.search(
+        r"ValueError: Make sure to provide either an '--scvi_reference_model' or a '--scanvi_reference_model', but not both.",
+        err.value.stdout.decode('utf-8')
+        )
+
+
 if __name__ == '__main__':
-    sys.exit(pytest.main([__file__]))
+    sys.exit(pytest.main([__file__]))

src/annotate/utils/query_reference_allignment.py

@@ -0,0 +1,46 @@
+import re
+
+import anndata as ad
+
+def setup_logger():
+    import logging
+    from sys import stdout
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+    console_handler = logging.StreamHandler(stdout)
+    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
+    console_handler.setFormatter(logFormatter)
+    logger.addHandler(console_handler)
+
+    return logger
+# END TEMPORARY WORKAROUND setup_logger
+logger = setup_logger()
+
+
+# Helper functions
+def set_var_index(adata: ad.AnnData, var_name: str | None = None):
+    if var_name:
+        adata.var.index = [re.sub("\\.[0-9]+$", "", s) for s in adata.var[var_name]]
+    else:
+        adata.var.index = [re.sub("\\.[0-9]+$", "", s) for s in adata.var.index]
+    return adata
+
+
+def cross_check_genes(query: ad.AnnData, reference: ad.AnnData):
+    logger.info("Detecting common vars based on gene ids")
+    common_ens_ids = list(set(reference.var.index).intersection(set(query.var.index)))
+
+    logger.info("  reference n_vars: %i", reference.n_vars)
+    logger.info("  input n_vars: %i", query.n_vars)
+    logger.info("  intersect n_vars: %i", len(common_ens_ids))
+    assert len(common_ens_ids) >= 100, "The intersection of genes between the query and reference dataset is too small."
+
+    return common_ens_ids
+
+
+def subset_vars(adata: ad.AnnData, var_column: str | None = None):
+    if var_column:
+        return adata[:, adata.var[var_column]]
+    else:
+        return adata

src/filter/subset_obsp/config.vsh.yaml

@@ -0,0 +1,75 @@
+name: subset_obsp
+namespace: "filter"
+description: |
+  Create a subset of an .obsp field in a mudata file, by filtering the columns based on the values of an .obs column. The resulting subset is moved to an .obsm slot.
+authors:
+  - __merge__: /src/authors/dorien_roosen.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Input
+    arguments:
+    - name: "--input"
+      type: file
+      description: Input h5mu file
+      direction: input
+      required: true
+      example: input.h5mu
+    - name: "--modality"
+      type: string
+      default: "rna"
+      required: false
+    - name: "--input_obsp_key"
+      type: string
+      required: true
+      description: The .obsp field to be filtered.
+    - name: "--input_obs_key"
+      type: string
+      required: true
+      description: The .obs column to filter on.
+    - name: "--input_obs_value"
+      type: string
+      required: true
+      description: The value to filter on in the .obs column.
+  - name: Output
+    arguments:
+    - name: "--output"
+      type: file
+      description: Output h5mu file.
+      direction: output
+      example: output.h5mu
+    - name: "--output_obsm_key"
+      type: string
+      required: true
+      description: The .obsm key to store the subset in.
+    - name: "--output_compression"
+      type: string
+      description: The compression format to be used on the output h5mu object.
+      choices: ["gzip", "lzf"]
+      required: false
+      example: "gzip"
+
+resources:
+  - type: python_script
+    path: script.py
+  - path: /src/utils/setup_logger.py
+test_resources:
+  - type: python_script
+    path: test.py
+  - path: /resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu
+
+engines:
+- type: docker
+  image: python:3.12-slim
+  setup:
+    - type: apt
+      packages: 
+        - procps
+    - type: python
+      __merge__: /src/base/requirements/anndata_mudata.yaml
+  __merge__: [ /src/base/requirements/python_test_setup.yaml, .]
+
+runners:
+- type: executable
+- type: nextflow
+  directives:
+    label: [singlecpu, lowmem]

src/filter/subset_obsp/script.py

@@ -0,0 +1,54 @@
+import mudata as mu
+
+### VIASH START
+par = {
+  'input': 'resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu',
+  'modality': 'rna',
+  'input_obsp_key': 'distances',
+  'input_obs_key': 'leiden',
+  'input_obs_value': '1',
+  'output_obsm_key': "leiden_1",
+  'output': 'subset_obsp_output.h5mu',
+  'output_compression': None,
+}
+### VIASH END
+
+# START TEMPORARY WORKAROUND setup_logger
+# reason: resources aren't available when using Nextflow fusion
+# from setup_logger import setup_logger
+def setup_logger():
+    import logging
+    from sys import stdout
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+    console_handler = logging.StreamHandler(stdout)
+    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
+    console_handler.setFormatter(logFormatter)
+    logger.addHandler(console_handler)
+
+    return logger
+# END TEMPORARY WORKAROUND setup_logger
+logger = setup_logger()
+
+def main():
+    logger.info(f"Reading {par['input']}")
+    mdata = mu.read_h5mu(par["input"])
+    adata = mdata.mod[par["modality"]]
+
+    logger.info(f"Subset columns of obsp matrix under {par['input_obsp_key']} based on {par['input_obs_key']} == {par['input_obs_value']}")
+    # .obsp, .obs and .obsm index and .obsp columns all have a dimension length of `n_obs`
+    # the index dimensions remain unaltered, but .obsp columns will be subset 
+    obsp = adata.obsp[par["input_obsp_key"]]
+    idx = adata.obs[par["input_obs_key"]].astype(str) == par["input_obs_value"]
+    obsm_subset = obsp[:, idx]
+
+    logger.info(f"Writing subset obsp matrix to .obsm {par['output_obsm_key']}")
+    adata.obsm[par["output_obsm_key"]] = obsm_subset
+
+    logger.info(f"Writing output to {par['output']}")
+    mdata.write_h5mu(par["output"], compression=par["output_compression"])
+
+
+if __name__ == '__main__':
+    main()

src/filter/subset_obsp/test.py

@@ -0,0 +1,48 @@
+import sys
+import pytest
+import mudata as mu
+
+## VIASH START
+meta = {
+    'resources_dir': 'resources_test/pbmc_1k_protein_v3/'
+}
+## VIASH END
+
+
+@pytest.fixture
+def input_h5mu():
+    input = mu.read_h5mu(f"{meta['resources_dir']}/pbmc_1k_protein_v3_mms.h5mu")
+    input.mod["rna"].obs["filter_column"] = "group_2"
+    input.mod["rna"].obs["filter_column"][:50] = "group_1"
+    return input
+
+
+@pytest.fixture
+def input_path(write_mudata_to_file, input_h5mu):
+    return write_mudata_to_file(input_h5mu)
+
+
+def test_subset_obsp(input_path, run_component, tmp_path):
+    output_path = tmp_path / "output.h5mu"
+
+    # run component
+    run_component([
+        "--input", input_path,
+        "--output", str(output_path),
+        "--input_obsp_key", "distances",
+        "--input_obs_key", "filter_column",
+        "--input_obs_value", "group_1",
+        "--output_obsm_key", "group_1"
+    ])
+
+    assert output_path.is_file(), "Output file not found"
+
+    # check output file
+    mu_out = mu.read_h5mu(output_path)
+
+    assert "group_1" in mu_out.mod["rna"].obsm, "Output should contain group_1 in .obsm"
+    assert mu_out.mod["rna"].obsm["group_1"].shape[1] == 50, "Obsm should only contain a subset of the original obsp matrix"
+
+
+if __name__ == "__main__":
+    sys.exit(pytest.main([__file__]))

src/labels_transfer/knn/config.vsh.yaml

@@ -1,7 +1,7 @@
-name: pynndescent_knn
+name: knn
 namespace: "labels_transfer"
 description: |
-  This component generates a neighborhood graph based using the PyNNDescentTransformer, followed by classification using a k-nearest neighborhood vote.
+  This component performs label transfer from reference to query using a K-Neirest Neighbors classifier.
 authors:
   - __merge__: /src/authors/dorien_roosen.yaml
     roles: [ maintainer, author ]
@@ -11,6 +11,27 @@ authors:
 __merge__: ../api/common_arguments.yaml
 
 argument_groups:
+  - name: Input dataset (query) arguments
+    arguments:
+      - name: "--input_obsm_distances"
+        type: string
+        direction: input
+        required: false
+        example: bbknn_distances
+        description: |
+          The `.obsm` key of the input (query) dataset containing pre-calculated distances. 
+          If not provided, the distances will be calculated using PyNNDescent.
+          Make sure the distance matrix contains distances relative to the reference dataset and were obtained in the same way as the reference embedding.
+
+  - name: Reference dataset arguments
+    arguments:
+      - name: "--reference_obsm_distances"
+        type: string
+        required: false
+        description: |
+          The `.obsm` key of the reference dataset containing pre-calculated distances. 
+          If not provided, the distances will be calculated using PyNNDescent.
+        example: bbknn_distances
 
   - name: KNN label transfer arguments
     arguments:
@@ -30,6 +51,7 @@ argument_groups:
         description: |
           The number of neighbors to use in k-neighbor graph structure used for fast approximate nearest neighbor search with PyNNDescent. 
           Larger values will result in more accurate search results at the cost of computation time.
+          
 resources:
   - type: python_script
     path: script.py
@@ -56,9 +78,7 @@ engines:
         packages:
           - pynndescent~=0.5.10
           - numpy<2
-    test_setup:
-      - type: python
-        __merge__: [ /src/base/requirements/viashpy.yaml ]
+    __merge__: [ /src/base/requirements/python_test_setup.yaml, .]
 
 runners:
   - type: executable

src/labels_transfer/knn/script.py

@@ -77,20 +77,46 @@ r_adata = r_mdata.mod[par["modality"]]
 logger.info("Checking arguments")
 par = check_arguments(par)
 
-# Generating training and inference data
-logger.info("Generating training and inference data")
-train_X = get_reference_features(r_adata, par, logger)
-inference_X = get_query_features(q_adata, par, logger)
+if par["input_obsm_distances"] and par["reference_obsm_distances"]:
+    logger.info("Using pre-calculated distances for KNN classification as provided in `--input_obsm_distances` and `--reference_obsm_distances`.")
 
-neighbors_transformer = PyNNDescentTransformer(
-    n_neighbors=par["n_neighbors"],
-    parallel_batch_queries=True,
-)
-neighbors_transformer.fit(train_X)
+    assert par["input_obsm_distances"] in q_adata.obsm, f"Make sure --input_obsm_distances {par['input_obsm_distances']} is a valid .obsm key. Found: {q_adata.obsm.keys()}."
+    assert par["reference_obsm_distances"] in r_adata.obsm, f"Make sure --reference_obsm_distances {par['reference_obsm_distances']} is a valid .obsm key. Found: {r_adata.obsm.keys()}."
 
-# Square sparse matrix with distances to n neighbors in reference data
-reference_neighbors = neighbors_transformer.transform(inference_X)
-query_neighbors = neighbors_transformer.transform(train_X)
+    query_neighbors = q_adata.obsm[par["input_obsm_distances"]]
+    reference_neighbors = r_adata.obsm[par["reference_obsm_distances"]]
+
+    if query_neighbors.shape[1] != reference_neighbors.shape[1]:
+        raise ValueError("The number of neighbors in the query and reference distance matrices do not match. Make sure both distance matrices contain distances to the reference dataset.")
+
+    # Make sure the number of neighbors present in the distance matrix matches the requested number of neighbors in --n_neighbors
+    # Otherwise reduce n_neighbors for KNN
+    smallest_neighbor_count = min(
+        np.diff(query_neighbors.indptr).min(),
+        np.diff(reference_neighbors.indptr).min()
+    )
+    if smallest_neighbor_count < par["n_neighbors"]:
+        logger.warning(f"The number of neighbors in the distance matrices is smaller than the requested number of neighbors in --n_neighbors. Reducing n_neighbors to {smallest_neighbor_count} for KNN Classification")
+        par["n_neighbors"] = smallest_neighbor_count
+
+elif par["input_obsm_distances"] or par["reference_obsm_distances"]:
+    raise ValueError("Make sure to provide both --input_obsm_distances and --reference_obsm_distances if you want to use a pre-calculated distance matrix for KNN classification.")
+
+elif not par["input_obsm_distances"] and not par["reference_obsm_distances"]:
+    logger.info("No pre-calculated distances were provided. Calculating distances using the PyNNDescent algorithm.")
+    # Generating training and inference data
+    train_X = get_reference_features(r_adata, par, logger)
+    inference_X = get_query_features(q_adata, par, logger)
+
+    neighbors_transformer = PyNNDescentTransformer(
+        n_neighbors=par["n_neighbors"],
+        parallel_batch_queries=True,
+    )
+    neighbors_transformer.fit(train_X)
+
+    # Square sparse matrix with distances to n neighbors in reference data
+    query_neighbors = neighbors_transformer.transform(inference_X)
+    reference_neighbors = neighbors_transformer.transform(train_X)
 
 # For each target, train a classifier and predict labels
 for obs_tar, obs_pred, obs_proba in zip(par["reference_obs_targets"],  par["output_obs_predictions"], par["output_obs_probability"]):
@@ -104,10 +130,14 @@ for obs_tar, obs_pred, obs_proba in zip(par["reference_obs_targets"],  par["outp
 
     logger.info(f"Using KNN classifier with {par['weights']} weights")
     train_y = r_adata.obs[obs_tar].to_numpy()
-    classifier = KNeighborsClassifier(n_neighbors=par["n_neighbors"], metric="precomputed", weights=weights_dict[par["weights"]])
-    classifier.fit(X=query_neighbors, y=train_y)
-    predicted_labels = classifier.predict(reference_neighbors)
-    probabilities = classifier.predict_proba(reference_neighbors).max(axis=1)
+    classifier = KNeighborsClassifier(
+        n_neighbors=par["n_neighbors"],
+        metric="precomputed",
+        weights=weights_dict[par["weights"]]
+        )
+    classifier.fit(X=reference_neighbors, y=train_y)
+    predicted_labels = classifier.predict(query_neighbors)
+    probabilities = classifier.predict_proba(query_neighbors).max(axis=1)
 
     # save_results
     logger.info(f"Saving predictions to {obs_pred} and probabilities to {obs_proba} in obs")

src/labels_transfer/knn/test.py

@@ -0,0 +1,155 @@
+import re
+import subprocess
+import pytest
+from pathlib import Path
+import anndata as ad
+import mudata as mu
+import numpy as np
+from scipy.sparse import csr_matrix
+
+## VIASH START
+meta = {
+    'resources_dir': './resources_test/'
+}
+## VIASH END
+
+reference_h5ad_file = f"{meta['resources_dir']}/annotation_test_data/TS_Blood_filtered.h5ad"
+# convert reference to h5mu
+reference_adata = ad.read_h5ad(reference_h5ad_file)
+reference_mdata = mu.MuData({"rna": reference_adata})
+reference_file = f"{meta['resources_dir']}/annotation_test_data/TS_Blood_filtered.h5mu"
+reference_mdata.write_h5mu(reference_file)
+input_file = f"{meta['resources_dir']}/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"
+
+
+def test_label_transfer(run_component, random_h5mu_path):
+    
+    output = random_h5mu_path()
+
+    args = [
+        "--input", input_file,
+        "--modality", "rna",
+        "--reference", reference_file,
+        "--reference_obs_targets", "cell_type",
+        "--output", output,
+        "--n_neighbors", "5"
+    ]
+
+    run_component(args)
+
+    assert Path(output).is_file()
+
+    output_data = mu.read_h5mu(output)
+
+    assert "cell_type_pred" in output_data.mod["rna"].obs, f"Predictions cell_type_pred is missing from output\noutput: {output_data.mod['rna'].obs}"
+    assert "cell_type_probability" in output_data.mod["rna"].obs, f"Uncertainties cell_type_probability is missing from output\noutput: {output_data.mod['rna'].obs}"
+
+
+@pytest.mark.parametrize("weights", ["uniform", "distance", "gaussian"])
+def test_label_transfer_prediction_columns(run_component, weights, random_h5mu_path):
+
+    output = random_h5mu_path()
+
+    args = [
+        "--input", input_file,
+        "--modality", "rna",
+        "--reference", reference_file,
+        "--reference_obs_targets", "cell_type",
+        "--weights", weights,
+        "--output", output,
+        "--output_obs_probability", "test_probability",
+        "--output_obs_predictions", "test_prediction",
+        "--n_neighbors", "5"
+    ]
+
+    run_component(args)
+
+    assert Path(output).is_file()
+
+    output_data = mu.read_h5mu(output)
+
+    assert "test_prediction" in output_data.mod["rna"].obs, f"Predictions test_prediction is missing from output\noutput: {output_data.mod['rna'].obs}"
+    assert "test_probability" in output_data.mod["rna"].obs, f"Uncertainties test_probability is missing from output\noutput: {output_data.mod['rna'].obs}"
+
+
+def test_label_transfer_prediction_precomputed_neighbor_graph(run_component, random_h5mu_path):
+
+    output = random_h5mu_path()
+
+    # Add mock distance matrix to obsm slot
+    reference_mdata = mu.read_h5mu(reference_file)
+    ref_distances = np.random.rand(400, 400)
+    ref_distances[ref_distances < 0.5] = 0
+    ref_distances = csr_matrix(ref_distances)
+    reference_mdata.mod["rna"].obsm["distances"] = ref_distances
+    reference_mdata.write_h5mu(reference_file)
+
+    query_mdata = mu.read_h5mu(input_file)
+    query_distances = np.random.rand(713, 400)
+    query_distances[query_distances < 0.5] = 0
+    query_distances = csr_matrix(query_distances)
+    query_mdata.mod["rna"].obsm["distances"] = query_distances
+    query_mdata.write_h5mu(input_file)
+
+    args = [
+        "--input", input_file,
+        "--modality", "rna",
+        "--reference", reference_file,
+        "--reference_obs_targets", "cell_type",
+        "--output", output,
+        "--input_obsm_distances", "distances",
+        "--reference_obsm_distances", "distances",
+        "--output_obs_probability", "test_probability",
+        "--output_obs_predictions", "test_prediction",
+        "--n_neighbors", "5"
+    ]
+
+    run_component(args)
+
+    assert Path(output).is_file()
+
+    output_data = mu.read_h5mu(output)
+
+    assert "test_prediction" in output_data.mod["rna"].obs, f"Predictions test_prediction is missing from output\noutput: {output_data.mod['rna'].obs}"
+    assert "test_probability" in output_data.mod["rna"].obs, f"Uncertainties test_probability is missing from output\noutput: {output_data.mod['rna'].obs}"
+
+
+def test_raises_distance_matrix_dimensions(run_component, random_h5mu_path):
+
+    output = random_h5mu_path()
+
+    reference_mdata = mu.read_h5mu(reference_file)
+    ref_distances = np.random.rand(400, 100)
+    ref_distances[ref_distances < 0.5] = 0
+    ref_distances = csr_matrix(ref_distances)
+    reference_mdata.mod["rna"].obsm["distances"] = ref_distances
+    reference_mdata.write_h5mu(reference_file)
+
+    query_mdata = mu.read_h5mu(input_file)
+    query_distances = np.random.rand(713, 400)
+    query_distances[query_distances < 0.5] = 0
+    query_distances = csr_matrix(query_distances)
+    query_mdata.mod["rna"].obsm["distances"] = query_distances
+    query_mdata.write_h5mu(input_file)
+
+    with pytest.raises(subprocess.CalledProcessError) as err:
+        run_component([
+            "--input", input_file,
+            "--modality", "rna",
+            "--reference", reference_file,
+            "--reference_obs_targets", "cell_type",
+            "--output", output,
+            "--input_obsm_distances", "distances",
+            "--reference_obsm_distances", "distances",
+            "--output_obs_probability", "test_probability",
+            "--output_obs_predictions", "test_prediction",
+            "--n_neighbors", "5"
+        ])
+    assert re.search(
+        r"ValueError: The number of neighbors in the query and reference distance matrices do not match. Make sure both distance matrices contain distances to the reference dataset.",
+        err.value.stdout.decode('utf-8')
+        )
+
+
+if __name__ == '__main__':
+    exit(pytest.main([__file__]))

src/labels_transfer/pynndescent_knn/test.py

@@ -1,70 +0,0 @@
-import pytest
-from pathlib import Path
-import anndata as ad
-import mudata as mu
-
-## VIASH START
-meta = {
-    'resources_dir': './resources_test/'
-}
-## VIASH END
-
-reference_h5ad_file = f"{meta['resources_dir']}/annotation_test_data/TS_Blood_filtered.h5ad"
-# convert reference to h5mu
-reference_adata = ad.read_h5ad(reference_h5ad_file)
-reference_mdata = mu.MuData({"rna": reference_adata})
-reference_file = f"{meta['resources_dir']}/annotation_test_data/TS_Blood_filtered.h5mu"
-reference_mdata.write_h5mu(reference_file)
-input_file = f"{meta['resources_dir']}/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"
-
-
-def test_label_transfer(run_component):
-
-    args = [
-        "--input", input_file,
-        "--modality", "rna",
-        "--reference", reference_file,
-        "--reference_obs_targets", "cell_type",
-        "--output", "output.h5mu",
-        "--n_neighbors", "5"
-    ]
-
-    run_component(args)
-
-    assert Path("output.h5mu").is_file()
-
-    output_data = mu.read_h5mu("output.h5mu")
-
-    assert "cell_type_pred" in output_data.mod["rna"].obs, f"Predictions cell_type_pred is missing from output\noutput: {output_data.mod['rna'].obs}"
-    assert "cell_type_probability" in output_data.mod["rna"].obs, f"Uncertainties cell_type_probability is missing from output\noutput: {output_data.mod['rna'].obs}"
-
-
-@pytest.mark.parametrize("weights", ["uniform", "distance", "gaussian"])
-def test_label_transfer_prediction_columns(run_component, weights):
-
-    output = f"output_{weights}.h5mu"
-
-    args = [
-        "--input", input_file,
-        "--modality", "rna",
-        "--reference", reference_file,
-        "--reference_obs_targets", "cell_type",
-        "--weights", weights,
-        "--output", output,
-        "--output_obs_probability", "test_probability",
-        "--output_obs_predictions", "test_prediction",
-        "--n_neighbors", "5"
-    ]
-
-    run_component(args)
-
-    assert Path(output).is_file()
-
-    output_data = mu.read_h5mu(output)
-
-    assert "test_prediction" in output_data.mod["rna"].obs, f"Predictions test_prediction is missing from output\noutput: {output_data.mod['rna'].obs}"
-    assert "test_probability" in output_data.mod["rna"].obs, f"Uncertainties test_probability is missing from output\noutput: {output_data.mod['rna'].obs}"
-
-
-if __name__ == '__main__':
-    exit(pytest.main([__file__]))

src/reference/build_bdrhap_reference/config.vsh.yaml

@@ -114,7 +114,7 @@ resources:
   - path: make_rhap_reference_2.2.1_nodocker.cwl
 test_resources:
   - type: bash_script
-    path: run_test.sh
+    path: test.sh
   - path: /resources_test/reference_gencodev41_chr1/reference.fa.gz
   - path: /resources_test/reference_gencodev41_chr1/reference.gtf.gz
 

src/reference/build_bdrhap_reference/test.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-
+set -eou pipefail
 
 ## VIASH START
 meta_executable="bin/viash run src/reference/make_reference/config.vsh.yaml --"

src/reference/build_cellranger_arc_reference/config.vsh.yaml

@@ -53,7 +53,7 @@ resources:
     path: script.sh
 test_resources:
   - type: bash_script
-    path: run_test.sh
+    path: test.sh
   - path: /resources_test/reference_gencodev41_chr1
 engines:
   - type: docker

src/reference/build_cellranger_arc_reference/script.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -eou pipefail
+set -eo pipefail
 
 ## VIASH START
 par_genome_fasta="resources_test/reference_gencodev41_chr1/reference.fa.gz"

src/reference/build_cellranger_reference/config.vsh.yaml

@@ -33,7 +33,7 @@ resources:
     path: script.sh
 test_resources:
   - type: bash_script
-    path: run_test.sh
+    path: test.sh
   - path: /resources_test/reference_gencodev41_chr1
 
 engines:

src/reference/build_cellranger_reference/script.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -eou pipefail
+set -eo pipefail
 
 ## VIASH START
 par_genome_fasta="resources_test/reference_gencodev41_chr1/reference.fa.gz"

src/reference/build_star_reference/test.sh

@@ -1,4 +1,6 @@
-# set -eo pipefail
+#!/bin/bash
+
+set -eou pipefail
 
 ## VIASH START
 meta_resources_dir="./resources_test"

src/reference/cellranger_mkgtf/config.vsh.yaml

@@ -27,8 +27,6 @@ resources:
   - type: bash_script
     path: script.sh
 test_resources:
-  # - type: bash_script
-  #   path: run_test.sh
   - type: python_script
     path: test.py
   - path: /resources_test/reference_gencodev41_chr1

src/reference/cellranger_mkgtf/run_test.sh

@@ -1,46 +0,0 @@
-#!/bin/bash
-
-set -eou pipefail
-
-## VIASH START
-meta_executable="bin/viash run src/reference/cellranger_mkgtf/config.vsh.yaml --"
-## VIASH END
-
-# create temporary directory
-tmpdir=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXXXX")
-function clean_up {
-    rm -rf "$tmpdir"
-}
-trap clean_up EXIT
-
-zcat "$meta_resources_dir/reference_gencodev41_chr1/reference.gtf.gz" | awk '$4 < 50001 {print ;}' | gzip > "$tmpdir/reference_small.gtf.gz"
-
-expected_gene_types=("transcribed_unprocessed_pseudogene" "miRNA")
-attribute_values=$(printf 'gene_type:%s,' "${expected_gene_types[@]}")
-attribute_values=${attribute_values%,}  # remove trailing comma
-echo $attribute_values
-
-echo "> Running $meta_name, writing to $tmpdir."
-$meta_executable \
-  --input_gtf "$tmpdir/reference_small.gtf.gz" \
-  --output_gtf "$tmpdir/myreference_filtered.gtf.gz" \
-  --attribute "$attribute_values" \
-  ---cpus ${meta_memory_gb:-1} \
-  ---memory ${meta_memory_gb:-2}GB
-
-exit_code=$?
-[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
-
-echo ">> Checking whether output can be found"
-[[ ! -f "$tmpdir/myreference_filtered.gtf.gz" ]] && echo "Output gtf file could not be found!" && exit 1
-
-echo ">> Checking attribute 'gene_type' in output gtf file"
-unique_gene_types=$(zcat "$tmpdir/myreference_filtered.gtf.gz" | awk -F'\t' '$9 ~ /gene_type/ { split($9, a, ";"); for(i in a) if(a[i] ~ /gene_type/) print a[i] }' | sed 's/.*gene_type "\(.*\)".*/\1/' | sort -u)
-echo "Expected gene types: ${expected_gene_types[@]}"
-echo "Unique gene types: $unique_gene_types"
-if [[ "${#expected_gene_types[@]}" != "$(echo "$unique_gene_types" | wc -w)" ]]; then
-  echo "Error: Not all expected gene types were found in the output gtf file"
-  exit 1
-fi
-
-echo "> Test succeeded!"

src/reference/cellranger_mkgtf/script.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -eou pipefail
+set -eo pipefail
 
 ## VIASH START
 par_input_gtf="resources_test/reference_gencodev41_chr1/reference.gtf.gz"

src/reference/make_reference/config.vsh.yaml

@@ -49,7 +49,7 @@ resources:
     path: script.sh
 test_resources:
   - type: bash_script
-    path: run_test.sh
+    path: test.sh
 engines:
   - type: docker
     image: ubuntu:22.04

src/reference/make_reference/run_test.sh

@@ -1,42 +0,0 @@
-#!/bin/bash
-
-set -eou pipefail
-
-## VIASH START
-meta_executable="bin/viash run src/reference/make_reference/config.vsh.yaml --"
-## VIASH END
-
-echo "> Running $meta_name."
-fasta="myreference.fa.gz"
-gtf="myreference.gtf.gz"
-
-wget https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz
-wget https://ftp.ensembl.org/pub/release-109/gtf/homo_sapiens/Homo_sapiens.GRCh38.109.chr.gtf.gz
-wget https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip
-
-$meta_executable \
-  --genome_fasta "Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz" \
-  --transcriptome_gtf "Homo_sapiens.GRCh38.109.chr.gtf.gz" \
-  --ercc "ERCC92.zip" \
-  --subset_regex "(ERCC-00002|1)" \
-  --output_fasta $fasta \
-  --output_gtf $gtf
-
-exit_code=$?
-[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
-
-echo ">> Checking whether output can be found"
-[[ ! -f $fasta ]] && echo "Output fasta file could not be found!" && exit 1
-[[ ! -f $gtf ]] && echo "Output gtf file could not be found!" && exit 1
-
-echo ">> Checking contents of fasta"
-if ! zgrep -q '>1' $fasta; then
-  echo "Could not find chromosome '1' in output reference!"
-  exit 1
-fi
-if ! zgrep -q '>ERCC-00002' $fasta; then
-  echo "Could not find ERCC-00002 in output reference!"
-  exit 1
-fi
-
-echo "> Test succeeded!"

src/reference/make_reference/script.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-set -eou pipefail
+set -eo pipefail
 
 ## VIASH START
 par_genome_fasta="https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz"

src/reference/make_reference/test.sh

@@ -0,0 +1,80 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+meta_executable="bin/viash run src/reference/make_reference/config.vsh.yaml --"
+## VIASH END
+
+# Fetch test data
+echo ">> Fetching test data"
+
+wget https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz
+wget https://ftp.ensembl.org/pub/release-109/gtf/homo_sapiens/Homo_sapiens.GRCh38.109.chr.gtf.gz
+wget https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip
+
+# Test 1
+echo ">> Test1"
+mkdir test1
+pushd test1
+fasta="myreference.fa.gz"
+gtf="myreference.gtf.gz"
+
+"$meta_executable" \
+  --genome_fasta "../Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz" \
+  --transcriptome_gtf "../Homo_sapiens.GRCh38.109.chr.gtf.gz" \
+  --ercc "../ERCC92.zip" \
+  --subset_regex "(ERCC-00002|1)" \
+  --output_fasta $fasta \
+  --output_gtf $gtf
+
+exit_code=$?
+[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
+
+echo ">> Checking whether output can be found"
+[[ ! -f $fasta ]] && echo "Output fasta file could not be found!" && exit 1
+[[ ! -f $gtf ]] && echo "Output gtf file could not be found!" && exit 1
+
+echo ">> Checking contents of fasta"
+if ! zgrep -q '>1' $fasta; then
+  echo "Could not find chromosome '1' in output reference!"
+  exit 1
+fi
+if ! zgrep -q '>ERCC-00002' $fasta; then
+  echo "Could not find ERCC-00002 in output reference!"
+  exit 1
+fi
+popd
+
+# Test 2
+echo ">> Test 2"
+mkdir test2
+pushd test2
+fasta="myreference.fa.gz"
+gtf="myreference.gtf.gz"
+
+"$meta_executable" \
+  --genome_fasta "../Homo_sapiens.GRCh38.dna.chromosome.1.fa.gz" \
+  --transcriptome_gtf "../Homo_sapiens.GRCh38.109.chr.gtf.gz" \
+  --output_fasta $fasta \
+  --output_gtf $gtf
+
+exit_code=$?
+[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
+
+echo ">> Checking whether output can be found"
+[[ ! -f $fasta ]] && echo "Output fasta file could not be found!" && exit 1
+[[ ! -f $gtf ]] && echo "Output gtf file could not be found!" && exit 1
+
+echo ">> Checking contents of fasta"
+if ! zgrep -q '>1' $fasta; then
+  echo "Could not find chromosome '1' in output reference!"
+  exit 1
+fi
+if zgrep -q '>ERCC-00002' $fasta; then
+  echo "Should not find ERCC-00002 in output reference!"
+  exit 1
+fi
+popd
+
+echo "> Test succeeded!"

src/workflows/gdo/gdo_singlesample/integration_test.sh

@@ -1,22 +1,16 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q gdo_singlesample
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/gdo/gdo_singlesample/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 

src/workflows/gdo/gdo_singlesample/main.nf

@@ -43,8 +43,7 @@ workflow run_wf {
         ]
         return newState
       },
-      toState: ["output": "output"],
-      auto: [ publish: true ]
+      toState: ["output": "output"]
     )
     | setState(["output"])
   emit:

src/workflows/gdo/gdo_singlesample/test.nf

@@ -5,13 +5,13 @@ include { gdo_singlesample } from params.rootDir + "/target/nextflow/workflows/g
 params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("10x_5k_lung_crispr/SC3_v3_NextGem_DI_CRISPR_A549_5K.h5mu"),
+        input: resources_test.resolve("10x_5k_lung_crispr/SC3_v3_NextGem_DI_CRISPR_A549_5K.h5mu"),
         min_counts: 3,
         max_counts: 10000000,
         min_guides_per_cell: 2,

src/workflows/ingestion/bd_rhapsody/integration_test.sh

@@ -1,22 +1,16 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/bd_rhapsody/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
+  -c src/workflows/utils/integration_tests.config 
 

src/workflows/ingestion/bd_rhapsody/test.nf

@@ -6,16 +6,16 @@ include { bd_rhapsody_test } from params.rootDir + "/target/nextflow/test_workfl
 params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList(
     [
       [
         id: "foo",
         reads: file("${params.resources_test}/bdrhap_5kjrt/raw/12*.fastq.gz"),
-        reference_archive: file(params.resources_test).resolve("reference_gencodev41_chr1/reference_bd_rhapsody.tar.gz"),
-        abseq_reference: file(params.resources_test).resolve("bdrhap_5kjrt/raw/BDAbSeq_ImmuneDiscoveryPanel.fasta"),
+        reference_archive: resources_test.resolve("reference_gencodev41_chr1/reference_bd_rhapsody.tar.gz"),
+        abseq_reference: resources_test.resolve("bdrhap_5kjrt/raw/BDAbSeq_ImmuneDiscoveryPanel.fasta"),
         cell_calling_data: "mRNA",
         exact_cell_count: 4900
       ] 

src/workflows/ingestion/cellranger_mapping/integration_test.sh

@@ -1,23 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q ingestion/cellranger_mapping --setup cb --platform nextflow
-
-export NXF_VER=21.10.6
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/cellranger_mapping/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
+  -c src/workflows/utils/integration_tests.config

src/workflows/ingestion/cellranger_mapping/main.nf

@@ -18,8 +18,7 @@ workflow run_wf {
       toState: [
         "input": "output",
         "output_raw": "output"
-      ],
-      auto: [ publish: true ]
+      ]
     )
     // split output dir into map
     | cellranger_count_split.run(
@@ -49,14 +48,9 @@ workflow run_wf {
           "input_metrics_summary": state.metrics_summary
         ]
       },
-      toState: { id, output, state ->
-        [
-          "output_raw": state.output_raw,
-          "output_h5mu": output.output
-        ]
-      },
-      auto: [ publish: true ],
+      toState: ["output_h5mu": "output"]
     )
+    | setState(["output_raw", "output_h5mu"])
 
   emit:
   output_ch

src/workflows/ingestion/cellranger_mapping/test.nf

@@ -7,11 +7,13 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [  
         id: "foo",
-        input: file(params.resources_test).resolve("cellranger_tiny_fastq/cellranger_tiny_fastq"),
-        reference: file(params.resources_test).resolve("cellranger_tiny_fastq/cellranger_tiny_ref"),
+        input: resources_test.resolve("cellranger_tiny_fastq/cellranger_tiny_fastq"),
+        reference: resources_test.resolve("cellranger_tiny_fastq/cellranger_tiny_ref"),
         output_type: "filtered",
       ]
     ])

src/workflows/ingestion/cellranger_multi/integration_test.sh

@@ -1,32 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=22.10.3
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/cellranger_multi/test.nf \
   -entry test_wf \
-  -resume \
-  -profile no_publish,docker \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
-
+  -c src/workflows/utils/integration_tests.config
 
 nextflow \
   run . \
   -main-script src/workflows/ingestion/cellranger_multi/test.nf \
   -entry test_wf2 \
-  -resume \
-  -profile no_publish,docker \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
+  -c src/workflows/utils/integration_tests.config

src/workflows/ingestion/cellranger_multi/test.nf

@@ -7,20 +7,32 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "foo",
-        input:[file(params.resources_test).resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_GEX_1_subset_S1_L001_R1_001.fastq.gz"),
-               file(params.resources_test).resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_GEX_1_subset_S1_L001_R2_001.fastq.gz"),
-               file(params.resources_test).resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_AB_subset_S2_L004_R1_001.fastq.gz"),
-               file(params.resources_test).resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_AB_subset_S2_L004_R2_001.fastq.gz"),
-               file(params.resources_test).resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_VDJ_subset_S1_L001_R1_001.fastq.gz"),
-               file(params.resources_test).resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_VDJ_subset_S1_L001_R2_001.fastq.gz")],
-        gex_reference: file(params.resources_test).resolve("reference_gencodev41_chr1/reference_cellranger.tar.gz"),
-        vdj_reference: file(params.resources_test).resolve("10x_5k_anticmv/raw/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0.tar.gz"),
-        feature_reference: file(params.resources_test).resolve("10x_5k_anticmv/raw/feature_reference.csv"),
-        library_id: ["5k_human_antiCMV_T_TBNK_connect_GEX_1_subset", "5k_human_antiCMV_T_TBNK_connect_AB_subset", "5k_human_antiCMV_T_TBNK_connect_VDJ_subset"],
-        library_type: ["Gene Expression", "Antibody Capture", "VDJ"]
+        input:[
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_GEX_1_subset_S1_L001_R1_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_GEX_1_subset_S1_L001_R2_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_AB_subset_S2_L004_R1_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_AB_subset_S2_L004_R2_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_VDJ_subset_S1_L001_R1_001.fastq.gz"),
+          resources_test.resolve("10x_5k_anticmv/raw/5k_human_antiCMV_T_TBNK_connect_VDJ_subset_S1_L001_R2_001.fastq.gz")
+        ],
+        gex_reference: resources_test.resolve("reference_gencodev41_chr1/reference_cellranger.tar.gz"),
+        vdj_reference: resources_test.resolve("10x_5k_anticmv/raw/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0.tar.gz"),
+        feature_reference: resources_test.resolve("10x_5k_anticmv/raw/feature_reference.csv"),
+        library_id: [
+          "5k_human_antiCMV_T_TBNK_connect_GEX_1_subset",
+          "5k_human_antiCMV_T_TBNK_connect_AB_subset",
+          "5k_human_antiCMV_T_TBNK_connect_VDJ_subset"
+        ],
+        library_type: [
+          "Gene Expression",
+          "Antibody Capture",
+          "VDJ"
+        ]
       ]
     ])
     | map{ state -> [state.id, state] }
@@ -44,8 +56,9 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // Test cell multiplexing
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "foo",

src/workflows/ingestion/cellranger_postprocessing/integration_test.sh

@@ -1,7 +1,5 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
@@ -14,9 +12,7 @@ nextflow \
   -entry test_wf \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt \
-  -resume
+  -c src/workflows/utils/integration_tests.config
 
 nextflow \
   run . \
@@ -24,6 +20,4 @@ nextflow \
   -entry test_wf2 \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt \
-  -resume
+  -c src/workflows/utils/integration_tests.config

src/workflows/ingestion/cellranger_postprocessing/main.nf

@@ -4,9 +4,10 @@ workflow run_wf {
 
   main:
   // perform correction if so desired
-  mid1_corrected = input_ch
-    | filter{ it[1].perform_correction }
+
+  output_ch = input_ch
     | cellbender_remove_background.run(
+      runIf: {id, state -> state.perform_correction},
       fromState: { id, state ->
         [
           input: state.input,
@@ -16,17 +17,13 @@ workflow run_wf {
         ]
       },
       toState: { id, output, state -> 
-        state + [input: output.output, layer: "cellbender_corrected"]
+        state + ["input": output.output, "layer": "cellbender_corrected"]
       }
     )
-  mid1_uncorrected = input_ch
-    | filter{ ! it[1].perform_correction }
-  mid1 = mid1_corrected.mix(mid1_uncorrected)
-
-  // perform filtering if so desired
-  mid2_filtered = mid1
-    | filter{ it[1].min_genes != null || it[1].min_counts != null }
     | filter_with_counts.run(
+      runIf: {id, state -> 
+        state.min_genes != null || state.min_counts != null
+      },
       fromState: { id, state ->
         [
           input: state.input,
@@ -39,16 +36,14 @@ workflow run_wf {
       },
       toState: [input: "output"]
     )
-  mid2_unfiltered = mid1
-    | filter{ it[1].min_genes == null && it[1].min_counts == null }
-  mid2 = mid2_filtered.mix(mid2_unfiltered)
-    
-  // return output map
-  output_ch = mid2
+    // Make sure to use the correct ouput file names, 
+    // irrespective wether or not any of the above 
+    // components were run
     | publish.run(
       fromState: [ input: "input", output: "output" ],
-      auto: [ publish: true ]
+      toState: ["output": "output"]
     )
+    | setState(["output"])
 
   emit:
   output_ch

src/workflows/ingestion/cellranger_postprocessing/test.nf

@@ -8,11 +8,13 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "foo",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
-        input_og: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
+        input_og: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
         perform_correction: true,
         min_genes: 100,
         min_counts: 1000,
@@ -55,9 +57,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
 
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [

src/workflows/ingestion/conversion/integration_test.sh

@@ -5,13 +5,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=24.04.4
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/conversion/test.nf \
   -entry test_wf \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -with-trace work/trace.txt
+  -c src/workflows/utils/integration_tests.config

src/workflows/ingestion/conversion/main.nf

@@ -25,11 +25,9 @@ workflow run_wf {
         }
         passed_state
       },
-      toState: {id, output, state, comp ->
-        ["output": output.output]
-      },
-      auto: [publish: true],
+      toState: ["output": "output"]
     )
+    | setState(["output": "output"])
   
   emit:
   output_ch

src/workflows/ingestion/conversion/test.nf

@@ -7,30 +7,32 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "10xh5_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5"),
         input_type: "10xh5",
         modality: null
       ],
       [
         id: "10xmtx_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix"),
         input_type: "10xmtx",
         modality: null,
         output: "\$id.h5mu"
       ],
       [
         id: "10xmtx",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix"),
         input_type: "10xmtx",
         modality: "rna",
         output: "\$key.h5mu"
       ],
       [
         id: "h5ad",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix_rna.h5ad"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix_rna.h5ad"),
         input_type: "h5ad",
         modality: "rna",
         output: "\$key.h5mu"

src/workflows/ingestion/demux/integration_test.sh

@@ -1,23 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q 'workflows/ingestion/demux'
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/demux/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
-  -with-trace work/trace.txt \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
+  -c src/workflows/utils/integration_tests.config

src/workflows/ingestion/demux/test.nf

@@ -7,24 +7,26 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   // or when running from s3:
   Channel.fromList([
     [
       id: "mkfastq_test",
-      input: file(params.resources_test).resolve("cellranger_tiny_bcl/bcl"),
-      sample_sheet: file(params.resources_test).resolve("cellranger_tiny_bcl/bcl/sample_sheet.csv"),
+      input: resources_test.resolve("cellranger_tiny_bcl/bcl"),
+      sample_sheet: resources_test.resolve("cellranger_tiny_bcl/bcl/sample_sheet.csv"),
       demultiplexer: "mkfastq"
     ],
     [
       id: "bclconvert_test",
-      input: file(params.resources_test).resolve("cellranger_tiny_bcl/bcl2/"),
-      sample_sheet: file(params.resources_test).resolve("cellranger_tiny_bcl/bcl2/sample_sheet.csv"),
+      input: resources_test.resolve("cellranger_tiny_bcl/bcl2/"),
+      sample_sheet: resources_test.resolve("cellranger_tiny_bcl/bcl2/sample_sheet.csv"),
       demultiplexer: "bclconvert"
     ],
     [
       id: "bcl2fastq_test",
-      input: file(params.resources_test).resolve("cellranger_tiny_bcl/bcl"),
-      sample_sheet: file(params.resources_test).resolve("cellranger_tiny_bcl/bcl/sample_sheet.csv"),
+      input: resources_test.resolve("cellranger_tiny_bcl/bcl"),
+      sample_sheet: resources_test.resolve("cellranger_tiny_bcl/bcl/sample_sheet.csv"),
       demultiplexer: "bcl2fastq",
       ignore_missing: true
     ]

src/workflows/ingestion/make_reference/integration_test.sh

@@ -1,20 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=23.04.2
-
 nextflow \
   run . \
   -main-script src/workflows/ingestion/make_reference/test.nf \
   -entry test_wf \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
+  -c src/workflows/utils/integration_tests.config

src/workflows/ingestion/make_reference/test.nf

@@ -6,12 +6,14 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "gencode_v41_ercc",
-        genome_fasta: file(params.resources_test).resolve("reference_gencodev41_chr1/reference.fa.gz"),
-        transcriptome_gtf: file(params.resources_test).resolve("reference_gencodev41_chr1/reference.gtf.gz"),
-        ercc: file(params.resources_test).resolve("reference_gencodev41_chr1/ERCC92.zip"),
+        genome_fasta: resources_test.resolve("reference_gencodev41_chr1/reference.fa.gz"),
+        transcriptome_gtf: resources_test.resolve("reference_gencodev41_chr1/reference.gtf.gz"),
+        ercc: resources_test.resolve("reference_gencodev41_chr1/ERCC92.zip"),
         subset_regex: "(ERCC-00002|chr1)",
         target: ["cellranger", "bd_rhapsody", "star"]
       ]        

src/workflows/integration/bbknn_leiden/integration_test.sh

@@ -1,25 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/bbknn_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/bbknn_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf2 \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
+  -c src/workflows/utils/integration_tests.config

src/workflows/integration/bbknn_leiden/main.nf

@@ -86,11 +86,9 @@ workflow run_wf {
           "output_compression": "gzip"
        ]
       },
-      toState: { id, output, state -> 
-        [ output: output.output ]
-      },
-      auto: [publish: true]
+      toState: ["output": "output"]
     )
+    | setState(["output"])
 
   emit:
   output_ch

src/workflows/integration/bbknn_leiden/test.nf

@@ -5,16 +5,19 @@ include { bbknn_leiden } from params.rootDir + "/target/nextflow/workflows/integ
 params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
+
+  resources_test = file(params.resources_test)
+
   output_ch =
     Channel.fromList([
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         layer: "log_normalized"
       ],
       [
        id: "no_leiden_resolutions_test",
-       input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+       input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
        layer: "log_normalized",
        leiden_resolution: []
       ]
@@ -45,7 +48,9 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
+
   output_ch =
     Channel.fromList([
       [

src/workflows/integration/harmony_leiden/integration_test.sh

@@ -1,27 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/harmony_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/harmony_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf2 \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config

src/workflows/integration/harmony_leiden/main.nf

@@ -77,11 +77,9 @@ workflow run_wf {
           "output_compression": "gzip"
         ]
       },
-      toState: { id, output, state ->
-        [ output: output.output ]
-      },
-      auto: [ publish: true ]
+      toState: ["output": "output"]
     )
+    | setState(["output"])
 
   emit:
   output_ch

src/workflows/integration/harmony_leiden/test.nf

@@ -6,11 +6,13 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = 
     Channel.fromList([
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         layer: "log_normalized",
         obs_covariates: "sample_id",
         embedding: "X_pca",
@@ -19,7 +21,7 @@ workflow test_wf {
       ],
       [
         id: "no_leiden_resolutions_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         layer: "log_normalized",
         obs_covariates: "sample_id",
         embedding: "X_pca",
@@ -53,7 +55,8 @@ workflow test_wf {
 
 
 workflow test_wf2 {
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = 
     Channel.fromList([

src/workflows/integration/scanorama_leiden/integration_test.sh

@@ -6,20 +6,18 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scanorama_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -resume \
-  -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-
-nextflow run . \
-  -main-script src/workflows/integration/scanorama_leiden/test.nf \
   -profile docker,no_publish \
-  -entry test_wf2 \
-  -resume \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
+  -c src/workflows/utils/integration_tests.config
+
+nextflow \
+  run . \
+  -main-script src/workflows/integration/scanorama_leiden/test.nf \
+  -entry test_wf2 \
+  -profile docker,no_publish \
+  -c src/workflows/utils/labels_ci.config \
+  -c src/workflows/utils/integration_tests.config

src/workflows/integration/scanorama_leiden/main.nf

@@ -74,11 +74,9 @@ workflow run_wf {
           "output_compression": "gzip"
         ]
       },
-      auto: [ publish: true ],
-      toState: { id, output, state ->
-        [ output: output.output ]
-      }
+      toState: ["output": "output"]
     )
+    | setState(["output"])
 
   emit:
   output_ch

src/workflows/integration/scanorama_leiden/test.nf

@@ -6,16 +6,18 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         layer: "log_normalized",
         leiden_resolution: [1.0, 0.25],
       ],
       [
         id: "no_leiden_resolutions_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         layer: "log_normalized",
         leiden_resolution: [],
       ]
@@ -46,8 +48,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [

src/workflows/integration/scgpt_leiden/integration_test.sh

@@ -1,29 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q scgpt_leiden
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scgpt_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scgpt_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf2 \
-  -resume \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
+  -c src/workflows/utils/integration_tests.config

src/workflows/integration/scgpt_leiden/main.nf

@@ -152,11 +152,9 @@ workflow run_wf {
           "output": state.workflow_output
         ]
       },
-      toState: { id, output, state ->
-        [ output: output.output ]
-      },
-      auto: [ publish: true ]
+      toState: ["output": "output"]
     )
+    | setState(["output"])
   
   emit:
     output_ch

src/workflows/integration/scgpt_leiden/test.nf

@@ -6,30 +6,32 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
     output_ch = Channel.fromList([
         [
-            id: "simple_execution_test",
-            input: file(params.resources_test).resolve("scgpt/test_resources/Kim2020_Lung_subset_preprocessed.h5mu"),
-            model: file(params.resources_test).resolve("scgpt/source/best_model.pt"),
-            model_config: file(params.resources_test).resolve("scgpt/source/args.json"),
-            model_vocab: file(params.resources_test).resolve("scgpt/source/vocab.json"),
-            input_layer: "log_normalized",
-            obs_batch_label: "sample",
-            n_hvg: 400,
-            seed: 1,
-            leiden_resolution: [1.0, 0.25]
+          id: "simple_execution_test",
+          input: resources_test.resolve("scgpt/test_resources/Kim2020_Lung_subset_preprocessed.h5mu"),
+          model: resources_test.resolve("scgpt/source/best_model.pt"),
+          model_config: resources_test.resolve("scgpt/source/args.json"),
+          model_vocab: resources_test.resolve("scgpt/source/vocab.json"),
+          input_layer: "log_normalized",
+          obs_batch_label: "sample",
+          n_hvg: 400,
+          seed: 1,
+          leiden_resolution: [1.0, 0.25]
         ],
         [
-            id: "no_leiden_resolutions_test",
-            input: file(params.resources_test).resolve("scgpt/test_resources/Kim2020_Lung_subset_preprocessed.h5mu"),
-            model: file(params.resources_test).resolve("scgpt/source/best_model.pt"),
-            model_config: file(params.resources_test).resolve("scgpt/source/args.json"),
-            model_vocab: file(params.resources_test).resolve("scgpt/source/vocab.json"),
-            obs_batch_label: "sample",
-            n_hvg: 400,
-            seed: 1,
-            input_layer: "log_normalized",
-            leiden_resolution: []
+          id: "no_leiden_resolutions_test",
+          input: resources_test.resolve("scgpt/test_resources/Kim2020_Lung_subset_preprocessed.h5mu"),
+          model: resources_test.resolve("scgpt/source/best_model.pt"),
+          model_config: resources_test.resolve("scgpt/source/args.json"),
+          model_vocab: resources_test.resolve("scgpt/source/vocab.json"),
+          obs_batch_label: "sample",
+          n_hvg: 400,
+          seed: 1,
+          input_layer: "log_normalized",
+          leiden_resolution: []
         ]
     ])
     | map{ state -> [state.id, state] }
@@ -59,7 +61,8 @@ workflow test_wf {
 
 
 workflow test_wf2 {
-  resources_test = file("${params.rootDir}/resources_test/scgpt")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [

src/workflows/integration/scvi_leiden/integration_test.sh

@@ -1,19 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/scvi_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
+  -c src/workflows/utils/integration_tests.config

src/workflows/integration/scvi_leiden/main.nf

@@ -98,14 +98,9 @@ workflow run_wf {
         "output_compression": "gzip"
         ]
       },
-      auto: [ publish: true ],
-      toState: { id, output, state ->
-        [ 
-          output: output.output, 
-          output_model: state.output_model
-        ]
-      }
+      toState: ["output": "output"] 
     )
+    | setState(["output", "output_model"])
 
   emit:
   output_ch

src/workflows/integration/scvi_leiden/test.nf

@@ -6,10 +6,12 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         layer: "log_normalized",
         obs_batch: "sample_id",
         max_epochs: 1,
@@ -17,7 +19,7 @@ workflow test_wf {
       ],
       [
         id: "no_leiden_resolutions_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         layer: "log_normalized",
         obs_batch: "sample_id",
         output_model: "no_leiden_resolutions_test_model/",

src/workflows/integration/totalvi_leiden/integration_test.sh

@@ -1,18 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=23.04.2
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/integration/totalvi_leiden/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config

src/workflows/integration/totalvi_leiden/main.nf

@@ -139,15 +139,9 @@ workflow run_wf {
           "compression": "gzip"
         ]
       },
-      toState: { id, output, state ->
-        [ 
-          output: output.output, 
-          reference_model_path: state.reference_model_path,
-          query_model_path: state.query_model_path
-        ]
-      },
-      auto: [ publish: true ]
+      toState: ["output", "output"]
     )
+    | setState(["output", "reference_model_path", "query_model_path"])
   emit:
   output_ch
 }

src/workflows/integration/totalvi_leiden/test.nf

@@ -6,11 +6,13 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
     output_ch = Channel.fromList([
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
-        reference: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        reference: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         prot_modality: "prot",
         prot_reference_modality: "prot",
         var_input: "filter_with_hvg",
@@ -21,8 +23,8 @@ workflow test_wf {
       ],
       [
         id: "no_prot_leiden_resolutions_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
-        reference: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        reference: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         prot_modality: "prot",
         prot_reference_modality: "prot",
         var_input: "filter_with_hvg",
@@ -34,8 +36,8 @@ workflow test_wf {
       ],
       [
         id: "no_rna_leiden_resolutions_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
-        reference: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        reference: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         prot_modality: "prot",
         prot_reference_modality: "prot",
         var_input: "filter_with_hvg",

src/workflows/multiomics/dimensionality_reduction/integration_test.sh

@@ -1,19 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/multiomics/dimensionality_reduction/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
+  -c src/workflows/utils/integration_tests.config

src/workflows/multiomics/dimensionality_reduction/main.nf

@@ -44,11 +44,9 @@ workflow run_wf {
           "output_compression": "gzip"
         ]
       },
-      toState: { id, output, state ->
-        [ output: output.output ]
-      },
-      auto: [ publish: true ]
+      toState: ["output": "output"]
     )
+    | setState(["output"])
 
   emit:
   output_ch

src/workflows/multiomics/dimensionality_reduction/test.nf

@@ -6,18 +6,19 @@ include { dimensionality_reduction_test } from params.rootDir + "/target/nextflo
 params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
-  // allow changing the resources_test dir
+
+  resources_test = file(params.resources_test)
 
   input_ch = Channel.fromList([
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
+        input: resources_test.resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
         layer: "",
         output: "foo.final.h5mu"
       ],
       [
         id: "pca_obsm_output_test",
-        input: file(params.resources_test).resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
+        input: resources_test.resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
         layer: "",
         output: "foo.final.h5mu"
       ],

src/workflows/multiomics/process_batches/integration_test.sh

@@ -1,26 +1,18 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q process_batches
-
-export NXF_VER=24.04.4
-
 nextflow \
   run . \
   -main-script src/workflows/multiomics/process_batches/test.nf \
   -entry test_wf \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
-
+  -c src/workflows/utils/integration_tests.config
 
 nextflow \
   run . \
@@ -28,5 +20,4 @@ nextflow \
   -entry test_wf2 \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config \
-  -resume
+  -c src/workflows/utils/integration_tests.config

src/workflows/multiomics/process_batches/main.nf

@@ -215,7 +215,7 @@ workflow run_wf {
             "output": state.workflow_output,
           ]
         },
-        auto: [publish: true]
+        toState: ["output": "output"]
       )
       | setState(["output"])
 

src/workflows/multiomics/process_batches/test.nf

@@ -9,16 +9,18 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   input_ch = Channel.fromList([
       [
           id: "test",
-          input: file(params.resources_test).resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
+          input: resources_test.resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
           publish_dir: "foo/",
           clr_axis: 0
       ],
       [
           id: "test2",
-          input: file(params.resources_test).resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
+          input: resources_test.resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
           publish_dir: "foo/",
           clr_axis: 1
       ]
@@ -52,8 +54,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   input_ch = Channel.fromList([
       [

src/workflows/multiomics/process_samples/integration_test.sh

@@ -8,15 +8,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=23.10.3
-
-viash ns build -q '^workflows'
-
 nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -26,7 +21,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config \
@@ -37,7 +31,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config \
@@ -48,7 +41,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config \
@@ -57,9 +49,8 @@ nextflow \
 nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
-  -entry test_wf2 \
-  -resume \
   -profile docker,no_publish \
+  -entry test_wf2 \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
@@ -67,7 +58,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf3 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -76,7 +66,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf4 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -85,7 +74,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf5 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -94,7 +82,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf6 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
@@ -103,7 +90,6 @@ nextflow \
   run . \
   -main-script src/workflows/multiomics/process_samples/test.nf \
   -entry test_wf7 \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
+  -c src/workflows/utils/integration_tests.config

src/workflows/multiomics/process_samples/test.nf

@@ -9,17 +9,19 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
     [
       id: "mouse",
-      input: file(params.resources_test).resolve("concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
+      input: resources_test.resolve("concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
       publish_dir: "foo/",
       rna_min_counts: 2,
       output: "test.h5mu",
     ],
     [
       id: "human",
-      input: file(params.resources_test).resolve("concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
+      input: resources_test.resolve("concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
       publish_dir: "foo/",
       rna_min_counts: 2,
       output: "test.h5mu",
@@ -42,8 +44,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -94,8 +96,8 @@ workflow test_wf2 {
 }
 
 workflow test_wf3 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   input_ch = Channel.fromList([
       [
@@ -156,8 +158,8 @@ workflow test_wf3 {
 }
 
 workflow test_wf4 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -187,8 +189,8 @@ workflow test_wf4 {
 }
 
 workflow test_wf5 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -235,8 +237,8 @@ workflow test_wf5 {
 }
 
 workflow test_wf6 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [
@@ -298,8 +300,8 @@ workflow test_wf6 {
 // }
 
 workflow test_wf7 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
     [

src/workflows/multiomics/split_modalities/integration_test.sh

@@ -4,12 +4,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-
-
-nextflow run . \
-    -main-script src/workflows/multiomics/split_modalities/test.nf \
-    -entry test_wf \
-    -resume \
-    -profile docker \
-    -c src/workflows/utils/labels_ci.config \
-    -c src/workflows/utils/integration_tests.config
+nextflow \
+  run . \
+  -main-script src/workflows/multiomics/split_modalities/test.nf \
+  -entry test_wf \
+  -profile docker,no_publish \
+  -c src/workflows/utils/labels_ci.config \
+  -c src/workflows/utils/integration_tests.config

src/workflows/multiomics/split_modalities/test.nf

@@ -7,10 +7,12 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
     [
       id: "mouse",
-      input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
+      input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
       publish_dir: "foo/",
       output: "modalities",
       output_types: "types.csv"

src/workflows/prot/prot_multisample/integration_test.sh

@@ -6,12 +6,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q prot_multisample
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/prot/prot_multisample/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
+  -c src/workflows/utils/integration_tests.config

src/workflows/prot/prot_multisample/test.nf

@@ -6,17 +6,19 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "adt_samples_axis_0",
         sample_id: "pbmc",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         clr_axis: 0
       ],
       [
         id: "adt_samples_axis_1",
         sample_id: "pbmc",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu"),
         clr_axis: 1
       ]
     ])

src/workflows/prot/prot_singlesample/integration_test.sh

@@ -6,15 +6,10 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q prot_singlesample
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/multiomics/prot_singlesample/test.nf \
-  -profile docker,no_publish \
-  -resume \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
-  -c src/workflows/utils/integration_tests.config
+  -c src/workflows/utils/integration_tests.config

src/workflows/prot/prot_singlesample/main.nf

@@ -44,7 +44,6 @@ workflow run_wf {
         return newState
       },
       toState: ["output": "output"],
-      auto: [ publish: true ]
     )
     | setState(["output"])
 

src/workflows/prot/prot_singlesample/test.nf

@@ -6,10 +6,12 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "foo",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
         min_counts: 3,
         max_counts: 100000,
         min_genes_per_cell: 2,

src/workflows/qc/qc/integration_test.sh

@@ -1,22 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q '^workflows/qc/qc'
-
 nextflow \
   run . \
   -main-script src/workflows/qc/qc/test.nf \
   -entry test_wf \
-  -resume \
   -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config

src/workflows/qc/qc/main.nf

@@ -81,7 +81,7 @@ workflow run_wf {
             "compression": "gzip"
           ]
         },
-        auto: [ publish: true ]
+        toState: ["output": "output"]
       )
       | setState(["output"]) 
 

src/workflows/qc/qc/test.nf

@@ -7,15 +7,17 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = 
     Channel.fromList([
       [
         id: "mouse_test",
-        input: file(params.resources_test).resolve("concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
+        input: resources_test.resolve("concat_test_data/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
       ],
       [
         id: "human_test",
-        input: file(params.resources_test).resolve("concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
+        input: resources_test.resolve("concat_test_data/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu"),
       ]
     ])
     | map { state -> [state.id, state] }

src/workflows/rna/rna_multisample/integration_test.sh

@@ -1,22 +1,15 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-viash ns build -q rna_multisample
-
-export NXF_VER=21.10.6
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/rna/rna_multisample/test.nf \
-  -profile docker,no_publish \
-  -resume \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config

src/workflows/rna/rna_multisample/test.nf

@@ -6,10 +6,12 @@ params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
 
+  resources_test = file(params.resources_test)
+
   output_ch = Channel.fromList([
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
+        input: resources_test.resolve("concat_test_data/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"),
         output: "concatenated_file.final.h5mu"
       ]
     ])

src/workflows/rna/rna_singlesample/integration_test.sh

@@ -1,30 +1,23 @@
 #!/bin/bash
 
-
-
 # get the root of the directory
 REPO_ROOT=$(git rev-parse --show-toplevel)
 
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-export NXF_VER=21.10.6
-
-viash ns build -q rna_singlesample
-# viash ns build -q 'filter|publish|qc|metadata' --parallel --setup cb
-
-nextflow run . \
+nextflow \
+  run . \
   -main-script src/workflows/rna/rna_singlesample/test.nf \
-  -profile docker,no_publish \
   -entry test_wf \
-  -with-trace work/trace.txt \
+  -profile docker,no_publish \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
-nextflow run . \
+nextflow \
+  run . \
+  -entry test_wf2 \
   -main-script src/workflows/rna/rna_singlesample/test.nf \
   -profile docker,no_publish \
-  -entry test_wf2 \
-  -with-trace work/trace.txt \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config

src/workflows/rna/rna_singlesample/main.nf

@@ -133,8 +133,8 @@ workflow run_wf {
         "layer": "layer",
       ],
       args: [output_compression: "gzip"],
-      auto: [ publish: true ]
     )
+    | setState(["output": "output"])
 
   emit:
   output_ch

src/workflows/rna/rna_singlesample/test.nf

@@ -5,13 +5,13 @@ include { rna_singlesample } from params.rootDir + "/target/nextflow/workflows/r
 params.resources_test = params.rootDir + "/resources_test"
 
 workflow test_wf {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [
         id: "mitochondrial_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
         min_counts: 3,
         max_counts: 10000000,
         min_genes_per_cell: 2,
@@ -27,7 +27,7 @@ workflow test_wf {
       ],
       [
         id: "simple_execution_test",
-        input: file(params.resources_test).resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
+        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
         min_counts: 3,
         max_counts: 10000000,
         min_genes_per_cell: 2,
@@ -54,8 +54,8 @@ workflow test_wf {
 }
 
 workflow test_wf2 {
-  // allow changing the resources_test dir
-  resources_test = file("${params.rootDir}/resources_test")
+
+  resources_test = file(params.resources_test)
 
   output_ch = Channel.fromList([
       [

src/workflows/test_workflows/qc/config.vsh.yaml

@@ -39,4 +39,6 @@ engines:
         __merge__: /src/base/requirements/viashpy.yaml
 runners:
   - type: executable
-  - type: nextflow
+  - type: nextflow
+    directives:
+      label: [midmem, midcpu]

target/executable/annotate/celltypist/.config.vsh.yaml

@@ -0,0 +1,427 @@
+name: "celltypist"
+namespace: "annotate"
+version: "fix-integration-tests"
+authors:
+- name: "Jakub Majercik"
+  roles:
+  - "author"
+  info:
+    role: "Contributor"
+    links:
+      email: "jakub@data-intuitive.com"
+      github: "jakubmajercik"
+      linkedin: "jakubmajercik"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatics Engineer"
+- name: "Weiwei Schultz"
+  roles:
+  - "contributor"
+  info:
+    role: "Contributor"
+    organizations:
+    - name: "Janssen R&D US"
+      role: "Associate Director Data Sciences"
+argument_groups:
+- name: "Inputs"
+  description: "Input dataset (query) arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "The input (query) data to be labeled. Should be a .h5mu file."
+    info: null
+    example:
+    - "input.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--modality"
+    description: "Which modality to process."
+    info: null
+    default:
+    - "rna"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_layer"
+    description: "The layer in the input data to be used for cell type annotation\
+      \ if .X is not to be used."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--var_query_gene_names"
+    description: "The name of the adata var column in the input data containing gene\
+      \ names; when no gene_name_layer is provided, the var index will be used.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Reference"
+  description: "Arguments related to the reference dataset."
+  arguments:
+  - type: "file"
+    name: "--reference"
+    description: "The reference data to train the CellTypist classifiers on. Only\
+      \ required if a pre-trained --model is not provided."
+    info: null
+    example:
+    - "reference.h5mu"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reference_layer"
+    description: "The layer in the reference data to be used for cell type annotation\
+      \ if .X is not to be used. Data are expected to be processed in the same way\
+      \ as the --input query dataset."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reference_obs_target"
+    description: "The name of the adata obs column in the reference data containing\
+      \ cell type annotations."
+    info: null
+    default:
+    - "cell_ontology_class"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--check_expression"
+    description: "Whether to check the expression of the reference dataset to the\
+      \ format reccomended by CellTypist.\nCellTypist requires data to be log-normalized\
+      \ to 10000 counts per cell.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--var_reference_gene_names"
+    description: "The name of the adata var column in the reference data containing\
+      \ gene names; when no gene_name_layer is provided, the var index will be used.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Model arguments"
+  description: "Model arguments."
+  arguments:
+  - type: "file"
+    name: "--model"
+    description: "Pretrained model in pkl format. If not provided, the model will\
+      \ be trained on the reference data and --reference should be provided."
+    info: null
+    example:
+    - "pretrained_model.pkl"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--feature_selection"
+    description: "Whether to perform feature selection."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--majority_voting"
+    description: "Whether to refine the predicted labels by running the majority voting\
+      \ classifier after over-clustering."
+    info: null
+    default:
+    - false
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "double"
+    name: "--C"
+    description: "Inverse of regularization strength in logistic regression."
+    info: null
+    default:
+    - 1.0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_iter"
+    description: "Maximum number of iterations before reaching the minimum of the\
+      \ cost function."
+    info: null
+    default:
+    - 1000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--use_SGD"
+    description: "Whether to use the stochastic gradient descent algorithm."
+    info: null
+    direction: "input"
+  - type: "double"
+    name: "--min_prop"
+    description: "\"For the dominant cell type within a subcluster, the minimum proportion\
+      \ of cells required to \nsupport naming of the subcluster by this cell type.\
+      \ Ignored if majority_voting is set to False. \nSubcluster that fails to pass\
+      \ this proportion threshold will be assigned 'Heterogeneous'.\"\n"
+    info: null
+    default:
+    - 0.0
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  description: "Output arguments."
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output h5mu file."
+    info: null
+    example:
+    - "output.h5mu"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_compression"
+    info: null
+    example:
+    - "gzip"
+    required: false
+    choices:
+    - "gzip"
+    - "lzf"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_obs_predictions"
+    description: "In which `.obs` slots to store the predicted information.\n"
+    info: null
+    default:
+    - "celltypist_pred"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_obs_probability"
+    description: "In which `.obs` slots to store the probability of the predictions.\n"
+    info: null
+    default:
+    - "celltypist_probability"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Automated cell type annotation tool for scRNA-seq datasets on the basis\
+  \ of logistic regression classifiers optimised by the stochastic gradient descent\
+  \ algorithm."
+test_resources:
+- type: "python_script"
+  path: "test.py"
+  is_executable: true
+- type: "file"
+  path: "annotation_test_data"
+- type: "file"
+  path: "pbmc_1k_protein_v3"
+- type: "file"
+  path: "openpipelinetestutils"
+  dest: "openpipelinetestutils"
+info: null
+status: "enabled"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "python:3.10-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "fix-integration-tests"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "libhdf5-dev"
+    - "procps"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "scanpy~=1.9.6"
+    upgrade: true
+  - type: "python"
+    user: false
+    packages:
+    - "celltypist==1.6.3"
+    upgrade: true
+  - type: "python"
+    user: false
+    packages:
+    - "anndata==0.10.8"
+    - "mudata~=0.2.4"
+    - "pandas!=2.1.2"
+    - "numpy<2.0.0"
+    upgrade: true
+  test_setup:
+  - type: "docker"
+    copy:
+    - "openpipelinetestutils /opt/openpipelinetestutils"
+  - type: "python"
+    user: false
+    packages:
+    - "/opt/openpipelinetestutils"
+    upgrade: true
+  - type: "python"
+    user: false
+    packages:
+    - "viashpy==0.8.0"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/annotate/celltypist/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/annotate/celltypist"
+  executable: "target/executable/annotate/celltypist/celltypist"
+  viash_version: "0.9.0"
+  git_commit: "da62b4ffe30b6ef36fcb7ef5944f29d45d1138ff"
+  git_remote: "https://x-access-token:ghs_WgbTvvspBKMSQ5BPucz45vMfHrxqK54Vys9e@github.com/openpipelines-bio/openpipeline"
+  git_tag: "0.2.0-1939-gda62b4ff"
+package_config:
+  name: "openpipeline"
+  version: "fix-integration-tests"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-data"
+      dest: "resources_test"
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
+    .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'fix-integration-tests'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline"
+    docker_registry: "ghcr.io"
+    homepage: "https://openpipelines.bio"
+    documentation: "https://openpipelines.bio/fundamentals"
+    issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"

target/executable/annotate/celltypist/nextflow_labels.config

@@ -0,0 +1,42 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}

target/executable/annotate/celltypist/setup_logger.py

@@ -0,0 +1,12 @@
+def setup_logger():
+    import logging
+    from sys import stdout
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+    console_handler = logging.StreamHandler(stdout)
+    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
+    console_handler.setFormatter(logFormatter)
+    logger.addHandler(console_handler)
+
+    return logger

target/executable/annotate/onclass/.config.vsh.yaml

@@ -0,0 +1,367 @@
+name: "onclass"
+namespace: "annotate"
+version: "fix-integration-tests"
+authors:
+- name: "Jakub Majercik"
+  roles:
+  - "author"
+  info:
+    role: "Contributor"
+    links:
+      email: "jakub@data-intuitive.com"
+      github: "jakubmajercik"
+      linkedin: "jakubmajercik"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Bioinformatics Engineer"
+argument_groups:
+- name: "Inputs"
+  description: "Input dataset (query) arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "The input (query) data to be labeled. Should be a .h5mu file."
+    info: null
+    example:
+    - "input.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--modality"
+    description: "Which modality to process."
+    info: null
+    default:
+    - "rna"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_layer"
+    description: "The layer in the input data to be used for cell type annotation\
+      \ if .X is not to be used."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--cl_nlp_emb_file"
+    description: "The .nlp.emb file with the cell type embeddings."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--cl_ontology_file"
+    description: "The .ontology file with the cell type ontology."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--cl_obo_file"
+    description: "The .obo file with the cell type ontology."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--var_query_gene_names"
+    description: "The name of the adata var column in the input data containing gene\
+      \ names; when no gene_name_layer is provided, the var index will be used.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Reference"
+  description: "Arguments related to the reference dataset."
+  arguments:
+  - type: "file"
+    name: "--reference"
+    description: "The reference data to train the CellTypist classifiers on. Only\
+      \ required if a pre-trained --model is not provided."
+    info: null
+    example:
+    - "reference.h5mu"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reference_layer"
+    description: "The layer in the reference data to be used for cell type annotation\
+      \ if .X is not to be used."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reference_obs_target"
+    description: "The name of the adata obs column in the reference data containing\
+      \ cell type annotations."
+    info: null
+    example:
+    - "cell_ontology_class"
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  description: "Output arguments."
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output h5mu file."
+    info: null
+    example:
+    - "output.h5mu"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_compression"
+    info: null
+    example:
+    - "gzip"
+    required: false
+    choices:
+    - "gzip"
+    - "lzf"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_obs_predictions"
+    description: "In which `.obs` slots to store the predicted information.\n"
+    info: null
+    default:
+    - "onclass_pred"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_obs_probability"
+    description: "In which `.obs` slots to store the probability of the predictions.\n"
+    info: null
+    default:
+    - "onclass_prob"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Model arguments"
+  description: "Model arguments"
+  arguments:
+  - type: "string"
+    name: "--model"
+    description: "\"Pretrained model path without a file extension. If not provided,\
+      \ the model will be trained \non the reference data and --reference should be\
+      \ provided. The path namespace should contain:\n  - a .npz or .pkl file\n  -\
+      \ a .data file\n  - a .meta file\n  - a .index file\ne.g. /path/to/model/pretrained_model_target1\
+      \ as saved by OnClass.\"\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--max_iter"
+    description: "Maximum number of iterations for training the model."
+    info: null
+    default:
+    - 30
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "OnClass is a python package for single-cell cell type annotation. It\
+  \ uses the Cell Ontology to capture the cell type similarity. \nThese similarities\
+  \ enable OnClass to annotate cell types that are never seen in the training data.\n"
+test_resources:
+- type: "python_script"
+  path: "test.py"
+  is_executable: true
+- type: "file"
+  path: "annotation_test_data"
+- type: "file"
+  path: "pbmc_1k_protein_v3"
+- type: "file"
+  path: "openpipelinetestutils"
+  dest: "openpipelinetestutils"
+info: null
+status: "enabled"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "python:3.8"
+  target_registry: "images.viash-hub.com"
+  target_tag: "fix-integration-tests"
+  namespace_separator: "/"
+  setup:
+  - type: "python"
+    user: false
+    packages:
+    - "scikit-learn==0.24.0"
+    - "OnClass==1.2"
+    - "tensorflow==2.13.1"
+    - "obonet==1.1.0"
+    - "mudata"
+    upgrade: true
+  test_setup:
+  - type: "docker"
+    copy:
+    - "openpipelinetestutils /opt/openpipelinetestutils"
+  - type: "python"
+    user: false
+    packages:
+    - "/opt/openpipelinetestutils"
+    upgrade: true
+  - type: "python"
+    user: false
+    packages:
+    - "viashpy==0.8.0"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/annotate/onclass/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/annotate/onclass"
+  executable: "target/executable/annotate/onclass/onclass"
+  viash_version: "0.9.0"
+  git_commit: "da62b4ffe30b6ef36fcb7ef5944f29d45d1138ff"
+  git_remote: "https://x-access-token:ghs_WgbTvvspBKMSQ5BPucz45vMfHrxqK54Vys9e@github.com/openpipelines-bio/openpipeline"
+  git_tag: "0.2.0-1939-gda62b4ff"
+package_config:
+  name: "openpipeline"
+  version: "fix-integration-tests"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-data"
+      dest: "resources_test"
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
+    .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'fix-integration-tests'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline"
+    docker_registry: "ghcr.io"
+    homepage: "https://openpipelines.bio"
+    documentation: "https://openpipelines.bio/fundamentals"
+    issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"

target/executable/annotate/onclass/nextflow_labels.config

@@ -0,0 +1,42 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}

target/executable/annotate/onclass/setup_logger.py

@@ -0,0 +1,12 @@
+def setup_logger():
+    import logging
+    from sys import stdout
+
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)
+    console_handler = logging.StreamHandler(stdout)
+    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
+    console_handler.setFormatter(logFormatter)
+    logger.addHandler(console_handler)
+
+    return logger

target/executable/annotate/popv/.config.vsh.yaml

@@ -0,0 +1,387 @@
+name: "popv"
+namespace: "annotate"
+version: "fix-integration-tests"
+authors:
+- name: "Matthias Beyens"
+  roles:
+  - "author"
+  info:
+    role: "Contributor"
+    links:
+      github: "MatthiasBeyens"
+      orcid: "0000-0003-3304-0706"
+      email: "matthias.beyens@gmail.com"
+      linkedin: "mbeyens"
+    organizations:
+    - name: "Janssen Pharmaceuticals"
+      href: "https://www.janssen.com"
+      role: "Principal Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "author"
+  info:
+    role: "Core Team Member"
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+argument_groups:
+- name: "Inputs"
+  description: "Arguments related to the input (aka query) dataset."
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Input h5mu file."
+    info: null
+    example:
+    - "input.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--modality"
+    description: "Which modality to process."
+    info: null
+    default:
+    - "rna"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_layer"
+    description: "Which layer to use. If no value is provided, the counts are assumed\
+      \ to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[input_layer]`."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_obs_batch"
+    description: "Key in obs field of input adata for batch information. If no value\
+      \ is provided, batch label is assumed to be unknown."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_var_subset"
+    description: "Subset the input object with this column."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_obs_label"
+    description: "Key in obs field of input adata for label information. This is only\
+      \ used for training scANVI. Unlabelled cells should be set to `\"unknown_celltype_label\"\
+      `."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--unknown_celltype_label"
+    description: "If `input_obs_label` is specified, cells with this value will be\
+      \ treated as unknown and will be predicted by the model."
+    info: null
+    default:
+    - "unknown"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Reference"
+  description: "Arguments related to the reference dataset."
+  arguments:
+  - type: "file"
+    name: "--reference"
+    description: "User-provided reference tissue. The data that will be used as reference\
+      \ to call cell types."
+    info: null
+    example:
+    - "TS_Bladder_filtered.h5ad"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reference_layer"
+    description: "Which layer to use. If no value is provided, the counts are assumed\
+      \ to be in the `.X` slot. Otherwise, count data is expected to be in `.layers[reference_layer]`."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reference_obs_label"
+    description: "Key in obs field of reference AnnData with cell-type information."
+    info: null
+    default:
+    - "cell_ontology_class"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--reference_obs_batch"
+    description: "Key in obs field of input adata for batch information."
+    info: null
+    default:
+    - "donor_assay"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  description: "Output arguments."
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output h5mu file."
+    info: null
+    example:
+    - "output.h5mu"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_compression"
+    info: null
+    example:
+    - "gzip"
+    required: false
+    choices:
+    - "gzip"
+    - "lzf"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  description: "Other arguments."
+  arguments:
+  - type: "string"
+    name: "--methods"
+    description: "Methods to call cell types. By default, runs to knn_on_scvi and\
+      \ scanvi."
+    info: null
+    example:
+    - "knn_on_scvi"
+    - "scanvi"
+    required: true
+    choices:
+    - "celltypist"
+    - "knn_on_bbknn"
+    - "knn_on_scanorama"
+    - "knn_on_scvi"
+    - "onclass"
+    - "rf"
+    - "scanvi"
+    - "svm"
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+- type: "file"
+  path: "setup_logger.py"
+- type: "file"
+  path: "nextflow_labels.config"
+  dest: "nextflow_labels.config"
+description: "Performs popular major vote cell typing on single cell sequence data\
+  \ using multiple algorithms. Note that this is a one-shot version of PopV."
+test_resources:
+- type: "python_script"
+  path: "test.py"
+  is_executable: true
+- type: "file"
+  path: "annotation_test_data"
+- type: "file"
+  path: "pbmc_1k_protein_v3"
+- type: "file"
+  path: "openpipelinetestutils"
+  dest: "openpipelinetestutils"
+info: null
+status: "enabled"
+links:
+  repository: "https://github.com/openpipelines-bio/openpipeline"
+  docker_registry: "ghcr.io"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    label:
+    - "highmem"
+    - "highcpu"
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+    script:
+    - "includeConfig(\"nextflow_labels.config\")"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "python:3.9-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "fix-integration-tests"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "git"
+    - "build-essential"
+    - "wget"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "scanpy~=1.9.6"
+    - "scvi-tools~=1.0.3"
+    - "popv~=0.3.2"
+    - "jax==0.4.10"
+    - "jaxlib==0.4.10"
+    - "ml-dtypes<0.3.0"
+    - "scipy==1.12.0"
+    upgrade: true
+  - type: "python"
+    user: false
+    packages:
+    - "anndata==0.10.8"
+    - "mudata~=0.2.4"
+    - "pandas!=2.1.2"
+    - "numpy<2.0.0"
+    upgrade: true
+  - type: "docker"
+    run:
+    - "cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git && \\\n\
+      \  cd PopV && git fetch --depth 1 origin tag v0.2 && git checkout v0.2\n"
+  test_setup:
+  - type: "python"
+    user: false
+    packages:
+    - "viashpy==0.8.0"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/annotate/popv/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/annotate/popv"
+  executable: "target/executable/annotate/popv/popv"
+  viash_version: "0.9.0"
+  git_commit: "da62b4ffe30b6ef36fcb7ef5944f29d45d1138ff"
+  git_remote: "https://x-access-token:ghs_WgbTvvspBKMSQ5BPucz45vMfHrxqK54Vys9e@github.com/openpipelines-bio/openpipeline"
+  git_tag: "0.2.0-1939-gda62b4ff"
+package_config:
+  name: "openpipeline"
+  version: "fix-integration-tests"
+  info:
+    test_resources:
+    - type: "s3"
+      path: "s3://openpipelines-data"
+      dest: "resources_test"
+  viash_version: "0.9.0"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".test_resources += {path: '/src/base/openpipelinetestutils', dest: 'openpipelinetestutils'}\n\
+    .resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n\
+    .runners[.type == 'nextflow'].directives.tag := '$id'\n.runners[.type == 'nextflow'].config.script\
+    \ := 'includeConfig(\"nextflow_labels.config\")'\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'fix-integration-tests'"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/openpipelines-bio/openpipeline"
+    docker_registry: "ghcr.io"
+    homepage: "https://openpipelines.bio"
+    documentation: "https://openpipelines.bio/fundamentals"
+    issue_tracker: "https://github.com/openpipelines-bio/openpipeline/issues"

target/executable/annotate/popv/nextflow_labels.config

@@ -0,0 +1,42 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+}
+
+def get_memory(to_compare) {
+  if (!process.containsKey("maxMemory") || !process.maxMemory) {
+    return to_compare
+  }
+
+  try {
+    if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+      return process.maxMemory
+    }
+    else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+      return max_memory as nextflow.util.MemoryUnit
+    }
+    else {
+      return to_compare
+    }  
+  } catch (all) {
+        println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+        System.exit(1)
+  }
+}