Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nFragment_file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nchromosome_sizes.tabular"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\ngene_annotation"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nBam-file"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Parameter\nKeys for annotations of obs/cells or vars/genes"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Dataset\nReplace_file"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["pp.import_data"];
  1 -->|output| 6;
  0 -->|output| 6;
  7["pp.make_fragment_file"];
  3 -->|output| 7;
  8["pl.frag_size_distr"];
  6 -->|anndata_out| 8;
  265d6020-44e2-408c-9eb6-02cbc9ac23a7["Output\nplot frag_size"];
  8 --> 265d6020-44e2-408c-9eb6-02cbc9ac23a7;
  style 265d6020-44e2-408c-9eb6-02cbc9ac23a7 stroke:#2c3143,stroke-width:4px;
  9["pl.frag_size_distr_log"];
  6 -->|anndata_out| 9;
  a37cd3c3-e07e-4bea-899f-ee44cee8370b["Output\nplot log frag_size"];
  9 --> a37cd3c3-e07e-4bea-899f-ee44cee8370b;
  style a37cd3c3-e07e-4bea-899f-ee44cee8370b stroke:#2c3143,stroke-width:4px;
  10["metrics.tsse"];
  6 -->|anndata_out| 10;
  2 -->|output| 10;
  233284e5-c184-4330-a1d3-2d03951c4ce7["Output\nanndata tsse"];
  10 --> 233284e5-c184-4330-a1d3-2d03951c4ce7;
  style 233284e5-c184-4330-a1d3-2d03951c4ce7 stroke:#2c3143,stroke-width:4px;
  11["pp.import_data-sorted_by_barcodes"];
  1 -->|output| 11;
  7 -->|fragments_out| 11;
  50ef9fe7-bb08-4957-bc45-079ed78f9ee8["Output\nanndata"];
  11 --> 50ef9fe7-bb08-4957-bc45-079ed78f9ee8;
  style 50ef9fe7-bb08-4957-bc45-079ed78f9ee8 stroke:#2c3143,stroke-width:4px;
  12["pl.tsse"];
  10 -->|anndata_out| 12;
  9a5c0f9c-0423-4822-871e-ba8317f2fa7b["Output\nplot tsse"];
  12 --> 9a5c0f9c-0423-4822-871e-ba8317f2fa7b;
  style 9a5c0f9c-0423-4822-871e-ba8317f2fa7b stroke:#2c3143,stroke-width:4px;
  13["pp.filter_cells"];
  10 -->|anndata_out| 13;
  b58dc4ad-6bf0-4f31-99f4-4f8deb13427c["Output\nanndata filter cells"];
  13 --> b58dc4ad-6bf0-4f31-99f4-4f8deb13427c;
  style b58dc4ad-6bf0-4f31-99f4-4f8deb13427c stroke:#2c3143,stroke-width:4px;
  14["pp.add_tile_matrix"];
  13 -->|anndata_out| 14;
  d4b64fc4-fd35-4781-b799-0d07fe8fe438["Output\nanndata tile matrix"];
  14 --> d4b64fc4-fd35-4781-b799-0d07fe8fe438;
  style d4b64fc4-fd35-4781-b799-0d07fe8fe438 stroke:#2c3143,stroke-width:4px;
  15["pp.select_features"];
  14 -->|anndata_out| 15;
  f531f6bd-3fc6-48b9-bb33-66de7928e670["Output\nanndata select features"];
  15 --> f531f6bd-3fc6-48b9-bb33-66de7928e670;
  style f531f6bd-3fc6-48b9-bb33-66de7928e670 stroke:#2c3143,stroke-width:4px;
  16["pp.scrublet"];
  15 -->|anndata_out| 16;
  5b17aa3a-3694-440f-9022-cf9761feb760["Output\nanndata scrublet"];
  16 --> 5b17aa3a-3694-440f-9022-cf9761feb760;
  style 5b17aa3a-3694-440f-9022-cf9761feb760 stroke:#2c3143,stroke-width:4px;
  17["pp.filter_doublets"];
  16 -->|anndata_out| 17;
  3838cf9d-a018-4aa7-8852-893b2f60ec2a["Output\nanndata filter doublets"];
  17 --> 3838cf9d-a018-4aa7-8852-893b2f60ec2a;
  style 3838cf9d-a018-4aa7-8852-893b2f60ec2a stroke:#2c3143,stroke-width:4px;
  18["tl.spectral"];
  17 -->|anndata_out| 18;
  77883516-8ac4-40b5-8b75-5750639d9fc4["Output\nanndata spectral"];
  18 --> 77883516-8ac4-40b5-8b75-5750639d9fc4;
  style 77883516-8ac4-40b5-8b75-5750639d9fc4 stroke:#2c3143,stroke-width:4px;
  19["tl.umap"];
  18 -->|anndata_out| 19;
  062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad["Output\nanndata umap"];
  19 --> 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad;
  style 062a5471-7b7a-4d9b-bf6c-fe9bbbc5d2ad stroke:#2c3143,stroke-width:4px;
  20["pp.knn"];
  19 -->|anndata_out| 20;
  b7ebe580-9938-48e5-8718-4df197126615["Output\nanndata knn"];
  20 --> b7ebe580-9938-48e5-8718-4df197126615;
  style b7ebe580-9938-48e5-8718-4df197126615 stroke:#2c3143,stroke-width:4px;
  21["tl.leiden"];
  20 -->|anndata_out| 21;
  9970eb96-013b-4d97-bbbf-2d1f4663b73c["Output\nanndata_leiden_clustering"];
  21 --> 9970eb96-013b-4d97-bbbf-2d1f4663b73c;
  style 9970eb96-013b-4d97-bbbf-2d1f4663b73c stroke:#2c3143,stroke-width:4px;
  22["pl.umap"];
  21 -->|anndata_out| 22;
  4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9["Output\numap_leiden-clusters"];
  22 --> 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9;
  style 4fff8ec8-7d6f-4871-9e42-d6c1791d6aa9 stroke:#2c3143,stroke-width:4px;
  23["make_gene_matrix"];
  21 -->|anndata_out| 23;
  2 -->|output| 23;
  9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a["Output\nanndata gene matrix"];
  23 --> 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a;
  style 9a5c2e23-5b59-41ae-aceb-0e47ce9e7b1a stroke:#2c3143,stroke-width:4px;
  24["scanpy_filter_genes"];
  23 -->|anndata_out| 24;
  7a9b22df-e0e5-49d9-9fa1-2efe316d6d66["Output\nanndata filter genes"];
  24 --> 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66;
  style 7a9b22df-e0e5-49d9-9fa1-2efe316d6d66 stroke:#2c3143,stroke-width:4px;
  25["Normalize"];
  24 -->|anndata_out| 25;
  7dddd4c8-1944-4f50-b331-857d03cc9631["Output\nanndata normalize"];
  25 --> 7dddd4c8-1944-4f50-b331-857d03cc9631;
  style 7dddd4c8-1944-4f50-b331-857d03cc9631 stroke:#2c3143,stroke-width:4px;
  26["pp.log1p"];
  25 -->|anndata_out| 26;
  40ace30a-21e1-4bf2-8e08-ad93b62fb2ee["Output\nanndata log1p"];
  26 --> 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee;
  style 40ace30a-21e1-4bf2-8e08-ad93b62fb2ee stroke:#2c3143,stroke-width:4px;
  27["external.pp.magic"];
  26 -->|anndata_out| 27;
  8c1c7aa9-b9dd-467b-9715-73773aea093f["Output\nanndata_magic"];
  27 --> 8c1c7aa9-b9dd-467b-9715-73773aea093f;
  style 8c1c7aa9-b9dd-467b-9715-73773aea093f stroke:#2c3143,stroke-width:4px;
  28["Copy obsm"];
  21 -->|anndata_out| 28;
  27 -->|anndata_out| 28;
  2c3825d3-7151-4eef-97d0-c8a31ca6fd3e["Output\nanndata_gene-matrix_leiden"];
  28 --> 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e;
  style 2c3825d3-7151-4eef-97d0-c8a31ca6fd3e stroke:#2c3143,stroke-width:4px;
  29["umap_plot_with_scanpy"];
  28 -->|output_h5ad| 29;
  4 -->|output| 29;
  4cfbbb70-156b-48d7-b14b-db21198d9b6d["Output\numap_marker-genes"];
  29 --> 4cfbbb70-156b-48d7-b14b-db21198d9b6d;
  style 4cfbbb70-156b-48d7-b14b-db21198d9b6d stroke:#2c3143,stroke-width:4px;
  30["Inspect observations"];
  28 -->|output_h5ad| 30;
  31["Cut leiden from table"];
  30 -->|obs| 31;
  11c22200-a54e-4585-82c4-8457dbbfb53c["Output\nleiden annotation"];
  31 --> 11c22200-a54e-4585-82c4-8457dbbfb53c;
  style 11c22200-a54e-4585-82c4-8457dbbfb53c stroke:#2c3143,stroke-width:4px;
  32["Replace leiden"];
  31 -->|out_file1| 32;
  5 -->|output| 32;
  467de061-79e6-4148-8a65-c06383a14012["Output\ncell type annotation"];
  32 --> 467de061-79e6-4148-8a65-c06383a14012;
  style 467de061-79e6-4148-8a65-c06383a14012 stroke:#2c3143,stroke-width:4px;
  33["Manipulate AnnData"];
  28 -->|output_h5ad| 33;
  32 -->|outfile_replace| 33;
  cbba6173-f439-4fd5-8423-946aa625112b["Output\nanndata_cell_type"];
  33 --> cbba6173-f439-4fd5-8423-946aa625112b;
  style cbba6173-f439-4fd5-8423-946aa625112b stroke:#2c3143,stroke-width:4px;
  34["Plot cell types"];
  33 -->|anndata| 34;
  c28c53ae-8ee7-47d7-8a00-352908bb7c1a["Output\numap_cell-type"];
  34 --> c28c53ae-8ee7-47d7-8a00-352908bb7c1a;
  style c28c53ae-8ee7-47d7-8a00-352908bb7c1a stroke:#2c3143,stroke-width:4px;
  35["Final Anndata general info"];
  33 -->|anndata| 35;
  379a85d1-a204-4b0b-8b33-86e5582fc51f["Output\ngeneral"];
  35 --> 379a85d1-a204-4b0b-8b33-86e5582fc51f;
  style 379a85d1-a204-4b0b-8b33-86e5582fc51f 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

• 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-standard-processing-snapatac2/workflows/Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.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