Add a new scRNA workflow for standard analysis using Scanpy #556

pavanvidem · 2024-10-09T12:11:51Z

Follows mostly the 3k PBMC clustering tutorial. It uses a workflow parameters file for some important parameters. All the plots automatically use the highly ranked genes.

bgruening · 2024-10-09T17:11:57Z

File [/home/runner/work/iwc/iwc/workflows/scRNAseq/standard-scanpy/test-data/Barcodes.txt] does not exist - parent directory [/home/runner/work/iwc/iwc/workflows/scRNAseq/standard-scanpy/test-data] does exist, cwd is [/home/runner/work/iwc/iwc]

The Barcodes file is missing.

bgruening · 2024-10-10T06:15:40Z

workflows/scRNAseq/standard-scanpy/Standard-scRNA-seq-with-Scanpy-tests.yml

+            keys: "uns/rank_genes_groups"
+    pl_umap_marker_genes:
+      path: test-data/pl_umap_marker_genes.png
+      compare: sim_size


There are nowadays better asserts available for images. Maybe you can add them in addition.

Also if you just compare sim_size you don't need to have the files in the repo, do you?

pavanvidem · 2024-10-11T16:16:24Z

@lldelisle can you please review this?

lldelisle

Looks great. Thanks.

lldelisle · 2024-10-14T07:33:34Z

workflows/scRNAseq/standard-scanpy/.dockstore.yml

+    orcid: 0000-0002-2799-424X
+  - name: Mehmet Tekman
+    orcid: 0000-0002-4181-2676
+  - name: "B\xE9r\xE9nice Batut"


Suggested change

- name: "B\xE9r\xE9nice Batut"

- name: "Bérénice Batut"

lldelisle · 2024-10-14T07:33:50Z

workflows/scRNAseq/standard-scanpy/README.md

+## Inputs dataset
+
+- The workflow needs 4 files as input
+    - A singl-cell count matrix file in Matrix Market Exchange format


Suggested change

- A singl-cell count matrix file in Matrix Market Exchange format

- A single-cell count matrix file in Matrix Market Exchange format

lldelisle · 2024-10-14T07:34:50Z

workflows/scRNAseq/standard-scanpy/README.md

+    - A singl-cell count matrix file in Matrix Market Exchange format
+    - A cell barcodes file with a single barcode in each line. The barcodes should correspond to the cells in the matrix file
+    - A genes/feature tabular file with gene ids and gene symbols
+


I think you forgot to describe the fourth file.

As well as the 3 input values

Good catch. But maybe we do not need a parameters file because @mvdbeek suggested using individual parameters instead of a file. We will have only 3 input files.

Yes indeed, but it would be good to describe the input values in the README.

lldelisle · 2024-10-14T07:36:18Z

workflows/scRNAseq/standard-scanpy/Standard-scRNA-seq-with-Scanpy.ga

+        {
+            "class": "Person",
+            "identifier": "0000-0001-9852-1987",
+            "name": "B\u00e9r\u00e9nice Batut"


Suggested change

"name": "B\u00e9r\u00e9nice Batut"

"name": "Bérénice Batut"

lldelisle · 2024-10-14T08:05:03Z

@mvdbeek Have you/we written down the naming convension for workflows?

mvdbeek · 2024-10-14T09:57:44Z

workflows/scRNAseq/standard-scanpy/.dockstore.yml

@@ -0,0 +1,17 @@
+version: 1.2
+workflows:
+- name: Standard-scRNA-seq-with-Scanpy


Suggested change

- name: Standard-scRNA-seq-with-Scanpy

- name: main

mvdbeek · 2024-10-14T09:58:53Z

workflows/scRNAseq/standard-scanpy/Standard-scRNA-seq-with-Scanpy-tests.yml

+    Annotate louvain clusters with these cell types: CD4+ T, CD14+, B, CD8+ T, FCGR3A+,
+      NK, Dendritic, Megakaryocytes
+  outputs:
+    initial_anndata_general_info:


Can you make all of these human readable please, no underscores. They are part of the primary output, so it should look nice.

I am renaming all the outputs. Is that still a problem in that case?

Yes. I don't think you need to rename the history items (but I don't mind of you do), workflow outputs should primarily be explored from the invocation view, not the history.

mvdbeek · 2024-10-14T10:00:48Z

workflows/scRNAseq/standard-scanpy/Standard-scRNA-seq-with-Scanpy.ga

+                    "name": "Workflow Params"
+                }
+            ],
+            "label": "Workflow Params",


This shouldn't be a file, but individual options.

mvdbeek · 2024-10-14T10:02:50Z

workflows/scRNAseq/standard-scanpy/Standard-scRNA-seq-with-Scanpy.ga

+    "format-version": "0.1",
+    "license": "CC-BY-4.0",
+    "release": "0.1",
+    "name": "Standard scRNA-seq with Scanpy",


Suggested change

"name": "Standard scRNA-seq with Scanpy",

"name": "scRNA-seq with Scanpy",

I will rename it to "Preprocessing and Clustering of single-cell RNA-seq data with Scanpy".

mvdbeek · 2024-10-14T10:03:20Z

workflows/scRNAseq/standard-scanpy/Standard-scRNA-seq-with-Scanpy.ga

@@ -0,0 +1,3096 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Standard scRNA-seq workflow with Scanpy and Anndata. Based on the 3k PBMC clustering tutorial from Scanpy. Important workflow parameters can be read from a tabular file.",


Please don't make the users write a parameter file, that's quite bad for UX, validation etc.

mvdbeek · 2024-10-14T10:06:59Z

I don't think we've agreed on anything yet. I would prefer to use Single Cell in the name field of the workflow itself.

mvdbeek · 2024-10-14T10:08:19Z

workflows/scRNAseq/standard-scanpy/README.md

@@ -0,0 +1,23 @@
+# Standard scRNA-seq Workflow using Scanpy and Anndata


What is even standard. Is clustering the thing you do here ?

Preprocessing and clustering. I will rename it accordingly.

bgruening · 2024-10-15T20:56:03Z

FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/iwc/iwc/workflows/scRNAseq/scanpy-clustering/test-data/General information about the final Anndata object.txt'

…ypes

pavanvidem added 4 commits October 9, 2024 14:08

Add a new scRNA workflow for standard analysis using Scanpy

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add release

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add .dockstore and README

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add png files and update tests

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pavanvidem added 2 commits October 9, 2024 23:41

replace file paths with links

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fix h5_keys

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bgruening reviewed Oct 10, 2024

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add image assertions and remove pngs from the test-data

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lldelisle reviewed Oct 14, 2024

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mvdbeek requested changes Oct 14, 2024

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mvdbeek reviewed Oct 14, 2024

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pavanvidem added 4 commits October 15, 2024 12:00

Apply suggestions and eloberate the README

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Add labels and rename files

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rename dir

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update .docstore.yml

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pavanvidem added 3 commits October 15, 2024 23:15

add missing test data

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Use pick param for optional params

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add release

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nekrut mentioned this pull request Oct 31, 2024

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Add a new scRNA workflow for standard analysis using Scanpy #556

Add a new scRNA workflow for standard analysis using Scanpy #556

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bgruening commented Oct 15, 2024

	- A singl-cell count matrix file in Matrix Market Exchange format
	- A single-cell count matrix file in Matrix Market Exchange format

	"name": "B\u00e9r\u00e9nice Batut"
	"name": "Bérénice Batut"

	"name": "Standard scRNA-seq with Scanpy",
	"name": "scRNA-seq with Scanpy",

		@@ -0,0 +1,23 @@
		# Standard scRNA-seq Workflow using Scanpy and Anndata

Add a new scRNA workflow for standard analysis using Scanpy #556

Are you sure you want to change the base?

Add a new scRNA workflow for standard analysis using Scanpy #556

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