Free up space in test data

resources_test_scripts/pbmc_1k_protein_v3.sh

@@ -45,11 +45,6 @@ target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu \
   --input "${OUT}_filtered_feature_bc_matrix.h5" \
   --input_metrics_summary "${OUT}_metrics_summary.csv" \
   --output "${OUT}_filtered_feature_bc_matrix.h5mu"
-
-target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu \
-  --input "${OUT}_raw_feature_bc_matrix.h5" \
-  --input_metrics_summary "${OUT}_metrics_summary.csv" \
-  --output "${OUT}_raw_feature_bc_matrix.h5mu"
 
 # run single sample
 NXF_VER=21.10.6 nextflow \

src/correction/cellbender_remove_background/config.vsh.yaml

@@ -274,7 +274,7 @@ functionality:
     - type: python_script
       path: test.py
     # normally cellbender should only be run on unfiltered data, but for the purposes of the unit test the filtered data will do.
-    - path: /resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_feature_bc_matrix.h5mu
+    - path: /resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu
 platforms:
   - type: docker
     image: nvcr.io/nvidia/cuda:11.8.0-devel-ubuntu22.04
@@ -296,6 +296,7 @@ platforms:
         packages:
           # Use this version of mudata because it is the last one that supports python 3.7
           - mudata~=0.2.1
+          - lxml[html_clean]
           - cellbender~=0.3.0
   - type: nextflow
     directives:

src/correction/cellbender_remove_background/script.py

@@ -7,7 +7,7 @@
 from scipy.sparse import csr_matrix
 from cellbender.remove_background.downstream import anndata_from_h5
 ## VIASH START
-file_input = "./resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_feature_bc_matrix.h5mu"
+file_input = "./resources_test/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"
 
 par = {
     # inputs

src/correction/cellbender_remove_background/test.py

@@ -9,7 +9,7 @@
 }
 ## VIASH END
 
-file_input = meta["resources_dir"] + "/pbmc_1k_protein_v3_raw_feature_bc_matrix.h5mu"
+file_input = meta["resources_dir"] + "/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu"
 file_output = "output.h5mu"
 
 print("> Check whether cellbender works when it should be working")

src/workflows/ingestion/cellranger_postprocessing/integration_test.sh

@@ -8,8 +8,6 @@ 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/cellranger_postprocessing/test.nf \

src/workflows/ingestion/cellranger_postprocessing/test.nf

@@ -11,8 +11,8 @@ workflow test_wf {
   output_ch = Channel.fromList([
       [
         id: "foo",
-        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_feature_bc_matrix.h5"),
-        input_og: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_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,
@@ -67,21 +67,15 @@ workflow test_wf2 {
   output_ch = Channel.fromList([
       [
         id: "zing",
-        input: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_feature_bc_matrix.h5"),
-        input_og: resources_test.resolve("pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_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: false,
         min_genes: 100,
         min_counts: 1000,
         cellbender_epochs: 5
       ]
     ])
     | map{ state -> [state.id, state] }
-    // first filter and convert to h5mu
-    | from_10xh5_to_h5mu.run(
-      fromState: ["input"],
-      toState: ["input": "output"]
-    )
-
     | cellranger_postprocessing.run(
       toState: {id, output, state ->
         output + [