Batch correction tutorial for single cell

topics/single-cell/tutorials/scrna_batch_correction/data-library.yaml

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+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Single Cell
+  description: Training material and practicals for all kinds of single cell analysis
+    (particularly scRNA-seq!). When you generate your lovely gene lists for your cells,
+    consider checking out our Transcriptomics tutorials for further network analysis!
+  items:
+  - name: Batch Correction and Integration with Seurat or Scanpy
+    items:
+    - name: 'DOI: 10.5281/zenodo.7311628'
+      description: latest
+      items:
+      - url: https://zenodo.org/records/14734574/files/Input_SeuratObject.rds
+        src: url
+        ext: rds
+        info: https://doi.org/10.5281/zenodo.14734574

topics/single-cell/tutorials/scrna_batch_correction/tutorial.bib

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+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@article{Ding2020,
+  title = {Systematic comparison of single-cell and single-nucleus RNA-sequencing methods},
+  volume = {38},
+  ISSN = {1546-1696},
+  url = {http://dx.doi.org/10.1038/s41587-020-0465-8},
+  DOI = {10.1038/s41587-020-0465-8},
+  number = {6},
+  journal = {Nature Biotechnology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Ding,  Jiarui and Adiconis,  Xian and Simmons,  Sean K. and Kowalczyk,  Monika S. and Hession,  Cynthia C. and Marjanovic,  Nemanja D. and Hughes,  Travis K. and Wadsworth,  Marc H. and Burks,  Tyler and Nguyen,  Lan T. and Kwon,  John Y. H. and Barak,  Boaz and Ge,  William and Kedaigle,  Amanda J. and Carroll,  Shaina and Li,  Shuqiang and Hacohen,  Nir and Rozenblatt-Rosen,  Orit and Shalek,  Alex K. and Villani,  Alexandra-Chloé and Regev,  Aviv and Levin,  Joshua Z.},
+  year = {2020},
+  month = apr,
+  pages = {737–746}
+}

topics/single-cell/tutorials/scrna_batch_correction/workflows/index.md

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+---
+layout: workflow-list
+---

topics/single-cell/tutorials/scrna_batch_correction/workflows/workflow_Seurat-test.yml

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+---
+- doc: Test sample data for the workflow
+  job:
+    Input_SeuratObject:
+      class: File
+      location: https://zenodo.org/records/14734574/files/Input_SeuratObject.rds
+      filetype: rds
+  outputs:
+    Inspect_before_Split: https://zenodo.org/records/14734574/files/Inspect_before_Split.txt
+      location: 
+      compare: diff
+    Inspect_after_Split:
+      location: https://zenodo.org/records/14734574/files/Inspect_after_Split.txt
+      compare: diff
+    UMAP_before_Split:
+      location: https://zenodo.org/records/14734574/files/UMAP_Before.png
+      compare: diff
+    UMAP_after_Split:
+      location: https://zenodo.org/records/14734574/files/UMAP_After.png
+      compare: diff