Quality_control_and_filtering_melanoma_xenium_workflow

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Europe
• Galaxy Australia
• Galaxy Canada
• Galaxy France
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nmelanoma_roi.spatialdata.zip"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["initial Anndata table"];
  0 -->|output| 1;
  2["Inspect AnnData"];
  1 -->|result_adata| 2;
  3["Inspect AnnData"];
  1 -->|result_adata| 3;
  4["QC metrics before filtering"];
  1 -->|result_adata| 4;
  480e466a-0f38-40d8-a144-9544b85e7bf0["Output\nQC metrics before filtering"];
  4 --> 480e466a-0f38-40d8-a144-9544b85e7bf0;
  style 480e466a-0f38-40d8-a144-9544b85e7bf0 stroke:#2c3143,stroke-width:4px;
  5["Violin_Plots_before_filteration"];
  4 -->|anndata_out| 5;
  6cc6c8ef-ec55-4fad-9cec-19ee7a046689["Output\nViolin_Plots_before_filteration"];
  5 --> 6cc6c8ef-ec55-4fad-9cec-19ee7a046689;
  style 6cc6c8ef-ec55-4fad-9cec-19ee7a046689 stroke:#2c3143,stroke-width:4px;
  6["Scatter plot before filtering"];
  4 -->|anndata_out| 6;
  68b0cadd-79b3-436a-b8ef-ff785b7b2659["Output\nScatter plot before filtering"];
  6 --> 68b0cadd-79b3-436a-b8ef-ff785b7b2659;
  style 68b0cadd-79b3-436a-b8ef-ff785b7b2659 stroke:#2c3143,stroke-width:4px;
  7["SpatialData with QC metrics"];
  0 -->|output| 7;
  4 -->|anndata_out| 7;
  8["Scanpy filter Minimum genes expressed"];
  4 -->|anndata_out| 8;
  47b83004-9657-421f-af26-fff91e232ff2["Output\nFilter minimum genes expressed"];
  8 --> 47b83004-9657-421f-af26-fff91e232ff2;
  style 47b83004-9657-421f-af26-fff91e232ff2 stroke:#2c3143,stroke-width:4px;
  9["Spatial Plot total_counts before filtering"];
  7 -->|spatialdata_output| 9;
  0d65f539-3c53-4486-bf86-34446d2f0130["Output\nSpatial Plot total_counts before filtering"];
  9 --> 0d65f539-3c53-4486-bf86-34446d2f0130;
  style 0d65f539-3c53-4486-bf86-34446d2f0130 stroke:#2c3143,stroke-width:4px;
  10["Spatial Plot n_genes_by_counts before filtering"];
  7 -->|spatialdata_output| 10;
  7efe5b5c-cef3-4d16-b7b3-ad219e5f308b["Output\nSpatial Plot n_genes_by_counts before filtering"];
  10 --> 7efe5b5c-cef3-4d16-b7b3-ad219e5f308b;
  style 7efe5b5c-cef3-4d16-b7b3-ad219e5f308b stroke:#2c3143,stroke-width:4px;
  11["Inspect AnnData"];
  8 -->|anndata_out| 11;
  12["Filter minimum number of counts of gene expressed"];
  8 -->|anndata_out| 12;
  3eeec312-343d-45dc-861e-8b2897774a73["Output\nFilter minimum number of counts of gene expressed"];
  12 --> 3eeec312-343d-45dc-861e-8b2897774a73;
  style 3eeec312-343d-45dc-861e-8b2897774a73 stroke:#2c3143,stroke-width:4px;
  13["Inspect AnnData"];
  12 -->|anndata_out| 13;
  14["Filter minimum number of cells expressed"];
  12 -->|anndata_out| 14;
  b7fd86f9-614c-40e7-bcfe-adf512b7d8f8["Output\nFilter minimum number of cells expressed"];
  14 --> b7fd86f9-614c-40e7-bcfe-adf512b7d8f8;
  style b7fd86f9-614c-40e7-bcfe-adf512b7d8f8 stroke:#2c3143,stroke-width:4px;
  15["Filter genes based on number of cells or counts Minimum number of counts"];
  14 -->|anndata_out| 15;
  b94fe64d-2fc6-4f03-8fe4-bd912045d7e2["Output\nFilter genes based on number of cells or counts Minimum number of counts"];
  15 --> b94fe64d-2fc6-4f03-8fe4-bd912045d7e2;
  style b94fe64d-2fc6-4f03-8fe4-bd912045d7e2 stroke:#2c3143,stroke-width:4px;
  16["Inspect AnnData"];
  15 -->|anndata_out| 16;
  17["Filter maximum number of counts"];
  15 -->|anndata_out| 17;
  cda1adb3-249e-4c41-9964-c7108943e2c1["Output\nFilter maximum number of counts"];
  17 --> cda1adb3-249e-4c41-9964-c7108943e2c1;
  style cda1adb3-249e-4c41-9964-c7108943e2c1 stroke:#2c3143,stroke-width:4px;
  18["Filter maximum number of genes expressed"];
  17 -->|anndata_out| 18;
  17e8e16f-fba2-449e-ad0c-c12df7691a94["Output\nFilter maximum number of genes expressed"];
  18 --> 17e8e16f-fba2-449e-ad0c-c12df7691a94;
  style 17e8e16f-fba2-449e-ad0c-c12df7691a94 stroke:#2c3143,stroke-width:4px;
  19["Inspect AnnData"];
  18 -->|anndata_out| 19;
  20["Filter cell_area more than 10"];
  18 -->|anndata_out| 20;
  acc71f7e-f132-4bd2-9e53-877e8770171b["Output\nFilter cell_area more than 10"];
  20 --> acc71f7e-f132-4bd2-9e53-877e8770171b;
  style acc71f7e-f132-4bd2-9e53-877e8770171b stroke:#2c3143,stroke-width:4px;
  21["Filter cell_area less than 400"];
  20 -->|anndata_out| 21;
  ca03e483-8b0f-44cb-b3ae-e15689b6f2c3["Output\nFilter cell_area less than 400"];
  21 --> ca03e483-8b0f-44cb-b3ae-e15689b6f2c3;
  style ca03e483-8b0f-44cb-b3ae-e15689b6f2c3 stroke:#2c3143,stroke-width:4px;
  22["Filtered AnnData table"];
  21 -->|anndata_out| 22;
  60870001-3a7c-4fbb-ab6b-970421fd652e["Output\nFiltered AnnData table"];
  22 --> 60870001-3a7c-4fbb-ab6b-970421fd652e;
  style 60870001-3a7c-4fbb-ab6b-970421fd652e stroke:#2c3143,stroke-width:4px;
  23["Violin_Plots_after_filteration"];
  22 -->|anndata_out| 23;
  99276f46-5390-4446-9125-2254860a5f4a["Output\nViolin_Plots_after_filteration"];
  23 --> 99276f46-5390-4446-9125-2254860a5f4a;
  style 99276f46-5390-4446-9125-2254860a5f4a stroke:#2c3143,stroke-width:4px;
  24["Scatter plot after filtering"];
  22 -->|anndata_out| 24;
  7bca78a9-9ce9-4ec4-9780-edb169e1f0a8["Output\nScatter plot after filtering"];
  24 --> 7bca78a9-9ce9-4ec4-9780-edb169e1f0a8;
  style 7bca78a9-9ce9-4ec4-9780-edb169e1f0a8 stroke:#2c3143,stroke-width:4px;
  25["SpatialData Operations"];
  0 -->|output| 25;
  22 -->|anndata_out| 25;
  26["Spatial Plot total_counts after filtering"];
  25 -->|spatialdata_output| 26;
  53ce37a0-b4b7-4cae-815e-7d559f9ffbcc["Output\nSpatial Plot after filtering"];
  26 --> 53ce37a0-b4b7-4cae-815e-7d559f9ffbcc;
  style 53ce37a0-b4b7-4cae-815e-7d559f9ffbcc stroke:#2c3143,stroke-width:4px;
  27["Spatial Plot table_processed after filtering"];
  25 -->|spatialdata_output| 27;
  7bca9117-c8ca-4e90-9460-6654be842c12["Output\nSpatial Plot table_processed after filtering"];
  27 --> 7bca9117-c8ca-4e90-9460-6654be842c12;
  style 7bca9117-c8ca-4e90-9460-6654be842c12 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. Provide your workflow
   • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
   • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/spatial-melanoma-SPICA/workflows/Quality-control-and-filtering-melanoma-xenium-workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows