Merge pull request #5638 from pavanvidem/scater-wf-test

Add workflow tests for Scater QC workflow

Author: shiltemann

topics/single-cell/tutorials/scrna-scater-qc/data-library.yaml

@@ -15,15 +15,15 @@ items:
     - name: 'DOI: 10.5281/zenodo.3386291'
       description: latest
       items:
-      - url: https://zenodo.org/api/files/83bb489c-cd94-4d33-b8f4-da1dd7ee8e2b/annotation.txt
+      - url: https://zenodo.org/records/3386291/files/annotation.txt
         src: url
         ext: txt
         info: https://doi.org/10.5281/zenodo.3386291
-      - url: https://zenodo.org/api/files/83bb489c-cd94-4d33-b8f4-da1dd7ee8e2b/counts.txt
+      - url: https://zenodo.org/records/3386291/files/counts.txt
         src: url
         ext: txt
         info: https://doi.org/10.5281/zenodo.3386291
-      - url: https://zenodo.org/api/files/83bb489c-cd94-4d33-b8f4-da1dd7ee8e2b/mt_controls.txt
+      - url: https://zenodo.org/records/3386291/files/mt_controls.txt
         src: url
         ext: txt
         info: https://doi.org/10.5281/zenodo.3386291

topics/single-cell/tutorials/scrna-scater-qc/tutorial.md

@@ -7,6 +7,10 @@ priority: 1
 redirect_from:
   - /topics/transcriptomics/tutorials/scrna-scater-qc/tutorial
 zenodo_link: 'https://zenodo.org/record/3386291'
+answer_histories:
+  - label: "UseGalaxy.eu"
+    history: https://singlecell.usegalaxy.eu/u/videmp/h/single-cell-qc-with-scater
+    date: 2024-12-12
 tags:
 questions:
 - How to ensure the quality of single-cell RNA-seq data?
@@ -32,12 +36,13 @@ time_estimation: 1H
 key_points:
 - Single-cell RNA-seq data is often noisy
 - scater can be used to apply the visualise-filter-visualise paradigm of quality control
-contributors:
-- ethering
-- nsoranzo
-
+contributions:
+  authorship:
+    - ethering
+    - nsoranzo
+  testing:
+    - pavanvidem
 gitter: Galaxy-Training-Network/galaxy-single-cell
-
 ---
 
 

topics/single-cell/tutorials/scrna-scater-qc/workflows/main_workflow-tests.yml

@@ -0,0 +1,35 @@
+- doc: Test outline for Single-cell-QC-with-scater
+  job:
+    annotation.txt:
+      class: File
+      location: https://zenodo.org/records/3386291/files/annotation.txt
+      filetype: tabular
+    counts.txt:
+      class: File
+      location: https://zenodo.org/records/3386291/files/counts.txt
+      filetype: tabular
+    mt_controls.txt:
+      class: File
+      location: https://zenodo.org/records/3386291/files/mt_controls.txt
+      filetype: txt
+  outputs:
+    lib_qc_plot:
+      asserts:
+        has_size:
+          value: 11291
+          delta: 500
+    output_loom:
+      asserts:
+        has_size:
+          value: 236352
+          delta: 10000
+    filtered_lib_qc_plot:
+      asserts:
+        has_size:
+          value: 10914
+          delta: 500
+    pca_plot:
+      asserts:
+        has_size:
+          value: 7106
+          delta: 350