update test resources, add changelog entry

Author: jakubmajercik

CHANGELOG.MD

@@ -1,3 +1,9 @@
+# openpipeline_qc x.x.x
+
+## MINOR CHANGES
+
+* Added support for Visium data ingestion and QC reporting (PR #16).
+
 # openpipeline_qc 0.2.0
 
 ## MINOR CHANGES

resources_test_scripts/spatial_qc_sample_data.sh

@@ -12,7 +12,7 @@ param_list:
   - id: Lung5_Rep2_tiny
     input: s3://openpipelines-bio/openpipeline_spatial/resources_test/cosmx/Lung5_Rep2_tiny.h5mu
   - id: visium_tiny
-    input: s3://openpipelines-bio/openpipeline_spatial/resources_test/visium/visium_tiny.h5mu
+    input: s3://openpipelines-bio/openpipeline_spatial/resources_test/visium/Visium_FFPE_Human_Ovarian_Cancer_tiny.h5mu
 var_name_mitochondrial_genes: mitochondrial
 var_name_ribosomal_genes: ribosomal
 output: '\$id.qc.h5mu'

src/workflows/generate_qc_report/config.vsh.yaml

@@ -135,9 +135,6 @@ test_resources:
   - type: nextflow_script
     path: test.nf
     entrypoint: test_xenium
-  - type: nextflow_script
-    path: test.nf
-    entrypoint: test_cosmx
   - type: nextflow_script
     path: test.nf
     entrypoint: test_visium

src/workflows/generate_qc_report/integration_test.sh

@@ -36,13 +36,6 @@ nextflow run . \
   -c src/configs/labels_ci.config \
   -resume
 
-nextflow run . \
-  -main-script src/workflows/generate_qc_report/test.nf \
-  -profile docker,no_publish,local \
-  -entry test_cosmx \
-  -c src/configs/labels_ci.config \
-  -resume
-
 nextflow run . \
   -main-script src/workflows/generate_qc_report/test.nf \
   -profile docker,no_publish,local \