Multisample Batch Correction with SnapATAC2 and Harmony

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Collection\nInput MultiSample Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nchrom_sizes"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ngencode.v46.annotation.gtf.gz"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["pp.import_data"];
  1 -->|output| 3;
  0 -->|output| 3;
  4["metrics.tsse"];
  3 -->|anndata_out| 4;
  2 -->|output| 4;
  5["pl.tsse"];
  4 -->|anndata_out| 5;
  a6e0e735-c13a-4560-9f99-d61f2d06a173["Output\ntsse-plots"];
  5 --> a6e0e735-c13a-4560-9f99-d61f2d06a173;
  style a6e0e735-c13a-4560-9f99-d61f2d06a173 stroke:#2c3143,stroke-width:4px;
  6["pp.filter_cells"];
  4 -->|anndata_out| 6;
  7["pp.add_tile_matrix"];
  6 -->|anndata_out| 7;
  8["pp.select_features"];
  7 -->|anndata_out| 8;
  9["pp.scrublet"];
  8 -->|anndata_out| 9;
  10["pp.filter_doublets"];
  9 -->|anndata_out| 10;
  11["Extract element identifiers"];
  10 -->|anndata_out| 11;
  12["Extract first dataset"];
  10 -->|anndata_out| 12;
  13["Select first"];
  11 -->|output| 13;
  14["Filter collection"];
  13 -->|out_file1| 14;
  10 -->|anndata_out| 14;
  dae74fe0-46fa-480a-832e-0d1c03e543c1["Output\ncollection_without_first_entry"];
  14 --> dae74fe0-46fa-480a-832e-0d1c03e543c1;
  style dae74fe0-46fa-480a-832e-0d1c03e543c1 stroke:#2c3143,stroke-width:4px;
  15["Concatenate AnnDatas"];
  12 -->|output| 15;
  14 -->|output_filtered| 15;
  16["pp.select_features on all"];
  15 -->|anndata| 16;
  17["tl.spectral"];
  16 -->|anndata_out| 17;
  18["tl.umap_no-batch-correction"];
  17 -->|anndata_out| 18;
  19["pl.umap_no-batch-correction"];
  18 -->|anndata_out| 19;
  c66faaf2-6d6b-4410-9eb1-13a25c101c93["Output\nout_png"];
  19 --> c66faaf2-6d6b-4410-9eb1-13a25c101c93;
  style c66faaf2-6d6b-4410-9eb1-13a25c101c93 stroke:#2c3143,stroke-width:4px;
  20["pp.harmony"];
  18 -->|anndata_out| 20;
  21["pp.mnn_correct"];
  18 -->|anndata_out| 21;
  22["pp.scanorama"];
  18 -->|anndata_out| 22;
  23["tl.umap_batch-correction"];
  20 -->|anndata_out| 23;
  24["tl.umap_mnn-correct"];
  21 -->|anndata_out| 24;
  25["tl.umap_scanorama"];
  22 -->|anndata_out| 25;
  26["UMAP-plot of X_spectral_harmony"];
  23 -->|anndata_out| 26;
  71f8f33f-0017-467e-bf8c-ccd0b213b731["Output\nx_spectral_harmony"];
  26 --> 71f8f33f-0017-467e-bf8c-ccd0b213b731;
  style 71f8f33f-0017-467e-bf8c-ccd0b213b731 stroke:#2c3143,stroke-width:4px;
  27["pp.knn"];
  23 -->|anndata_out| 27;
  28["UMAP-plot of X_spectral_mnn-correct"];
  24 -->|anndata_out| 28;
  2fa7f3dc-fed8-4a34-b857-4cfd276e7625["Output\nx_spectral_mnn-correct"];
  28 --> 2fa7f3dc-fed8-4a34-b857-4cfd276e7625;
  style 2fa7f3dc-fed8-4a34-b857-4cfd276e7625 stroke:#2c3143,stroke-width:4px;
  29["UMAP plot of X_spectral_scanorama"];
  25 -->|anndata_out| 29;
  7a6c6165-42b6-4fff-b0d5-35f94541cd79["Output\nx_spectral_scanorma"];
  29 --> 7a6c6165-42b6-4fff-b0d5-35f94541cd79;
  style 7a6c6165-42b6-4fff-b0d5-35f94541cd79 stroke:#2c3143,stroke-width:4px;
  30["tl.leiden"];
  27 -->|anndata_out| 30;
  532c487d-bfdb-4552-bed2-17ca6063aa01["Output\nanndata_harmony_leiden"];
  30 --> 532c487d-bfdb-4552-bed2-17ca6063aa01;
  style 532c487d-bfdb-4552-bed2-17ca6063aa01 stroke:#2c3143,stroke-width:4px;
  31["UMAP-plot of Leiden Clusters"];
  30 -->|anndata_out| 31;

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

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• 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”
• 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/scatac-batch-correction-snapatac2/workflows/main_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