Workflows
These workflows are associated with Single-cell ATAC-seq standard processing with SnapATAC2
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.
Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2
Timon Schlegel
Last updated Aug 9, 2024
Launch in Tutorial Mode
License:
CC-BY-4.0
Tests: ✅
Results: Not yet automated
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;
Importing into Galaxy
Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!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:
Video: Importing a workflow from URL