fix tests

Author: dorien-er

src/workflows/multiomics/process_singlesample/integration_test.sh

@@ -32,6 +32,14 @@ nextflow \
   -c src/workflows/utils/labels_ci.config \
   -c src/workflows/utils/integration_tests.config
 
+nextflow \
+  run . \
+  -main-script src/workflows/multiomics/process_singlesample/test.nf \
+  -entry test_wf4 \
+  -profile docker,no_publish \
+  -c src/workflows/utils/labels_ci.config \
+  -c src/workflows/utils/integration_tests.config
+
 nextflow \
   run . \
   -main-script src/workflows/multiomics/process_singlesample/test.nf \

src/workflows/multiomics/process_singlesample/test.nf

@@ -172,69 +172,6 @@ workflow test_wf4 {
 
   resources_test = file(params.resources_test)
 
-  input_ch = Channel.fromList([
-    [
-      id: "pbmc",
-      input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
-      rna_min_counts: 2,
-      rna_max_counts: 1000000,
-      rna_min_genes_per_cell: 1,
-      rna_max_genes_per_cell: 1000000,
-      rna_min_percentile_counts: 0.05,
-      rna_max_percentile_counts: 0.95,
-      rna_min_cells_per_gene: 1,
-      rna_min_fraction_mito: 0.0,
-      rna_max_fraction_mito: 1.0,
-      prot_min_counts: 3,
-      prot_max_counts: 1000000,
-      prot_min_percentile_counts: 0.05,
-      prot_max_percentile_counts: 0.95,
-      prot_min_proteins_per_cell: 1,
-      prot_max_proteins_per_cell: 1000000,
-      prot_min_cells_per_protein: 1,
-      var_name_mitochondrial_genes: 'mitochondrial',
-      obs_name_mitochondrial_fraction: 'fraction_mitochondrial',
-      var_name_ribosomal_genes: 'ribosomal',
-      obs_name_ribosomal_fraction: 'fraction_ribosomal',
-      add_id_to_obs: true,
-      add_id_make_observation_keys_unique: true,
-      do_subset: true,
-      add_id_obs_output: "sample_id",
-      intersect_obs: true,
-      skip_qc_metrics: true,
-      output: "pbmc_test.h5mu"
-    ]
-  ])
-  | map{ state -> [state.id, state] }
-  | process_singlesample.run(
-    toState: { id, output, state -> output + [orig_input: state.input] }
-  )
-
-  assert_ch = input_ch
-  | view { output ->
-    assert output.size() == 2 : "outputs should contain two elements; [id, file]"
-    assert output[1].output.toString().endsWith("pbmc_test.h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
-    "Output: $output"
-  }
-  | toSortedList()
-  | map { output_list ->
-    assert output_list.size() == 1 : "output channel should contain one event, got ${output_list.size()}"
-    assert output_list[0][0] == "pbmc" : "Output id should be `pbmc`."
-  }
-
-  test_ch = input_ch
-    | workflow5_test.run(
-      fromState: [
-        "input": "output",
-        "orig_input": "orig_input"
-      ],
-    )
-}
-
-workflow test_wf5 {
-
-  resources_test = file(params.resources_test)
-
   // Shared single-sample processing parameters. QC metrics are calculated
   def base_args = [
     input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
@@ -326,3 +263,66 @@ workflow test_wf5 {
       }
     )
 }
+
+workflow test_wf5 {
+
+  resources_test = file(params.resources_test)
+
+  input_ch = Channel.fromList([
+    [
+      id: "pbmc",
+      input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"),
+      rna_min_counts: 2,
+      rna_max_counts: 1000000,
+      rna_min_genes_per_cell: 1,
+      rna_max_genes_per_cell: 1000000,
+      rna_min_percentile_counts: 0.05,
+      rna_max_percentile_counts: 0.95,
+      rna_min_cells_per_gene: 1,
+      rna_min_fraction_mito: 0.0,
+      rna_max_fraction_mito: 1.0,
+      prot_min_counts: 3,
+      prot_max_counts: 1000000,
+      prot_min_percentile_counts: 0.05,
+      prot_max_percentile_counts: 0.95,
+      prot_min_proteins_per_cell: 1,
+      prot_max_proteins_per_cell: 1000000,
+      prot_min_cells_per_protein: 1,
+      var_name_mitochondrial_genes: 'mitochondrial',
+      obs_name_mitochondrial_fraction: 'fraction_mitochondrial',
+      var_name_ribosomal_genes: 'ribosomal',
+      obs_name_ribosomal_fraction: 'fraction_ribosomal',
+      add_id_to_obs: true,
+      add_id_make_observation_keys_unique: true,
+      do_subset: true,
+      add_id_obs_output: "sample_id",
+      intersect_obs: true,
+      skip_qc_metrics: true,
+      output: "pbmc_test.h5mu"
+    ]
+  ])
+  | map{ state -> [state.id, state] }
+  | process_singlesample.run(
+    toState: { id, output, state -> output + [orig_input: state.input] }
+  )
+
+  assert_ch = input_ch
+  | view { output ->
+    assert output.size() == 2 : "outputs should contain two elements; [id, file]"
+    assert output[1].output.toString().endsWith("pbmc_test.h5mu") : "Output file should be a h5mu file. Found: ${output[1].output}"
+    "Output: $output"
+  }
+  | toSortedList()
+  | map { output_list ->
+    assert output_list.size() == 1 : "output channel should contain one event, got ${output_list.size()}"
+    assert output_list[0][0] == "pbmc" : "Output id should be `pbmc`."
+  }
+
+  test_ch = input_ch
+    | workflow5_test.run(
+      fromState: [
+        "input": "output",
+        "orig_input": "orig_input"
+      ],
+    )
+}