Workflows
These workflows are associated with Generating a single cell matrix using Alevin
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.
Generating a single cell matrix using Alevin 1.9
Wendi Bacon, Julia Jakiela
Last updated May 15, 2023
Launch in Tutorial Mode
License:
CC-BY-4.0
Tests: ✅
Results: Not yet automated
flowchart TD 0["ℹ️ Input Dataset\nRead 1 - containing cell barcode & UMI"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nRead 2 - containing transcript"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nMus_musculus.GRCm38.cdna.all.fa"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nMus_musculus.GRCm38.100.gtf.gz"]; style 3 stroke:#2c3143,stroke-width:4px; 4["Transcript-gene mapping"]; 2 -->|output| 4; 3 -->|output| 4; 5["Gene information"]; 3 -->|output| 5; 6["Alevin Processed"]; 0 -->|output| 6; 1 -->|output| 6; 4 -->|fasta_output| 6; 4 -->|feature_annotation| 6; 7["Alevin - no processing"]; 0 -->|output| 7; 1 -->|output| 7; 4 -->|fasta_output| 7; 4 -->|feature_annotation| 7; 8["Droplet rank plot - Alevin barcodes"]; 6 -->|quants_mat_mtx| 8; 9["Droplet rank plot - raw barcodes"]; 6 -->|raw_cb_frequency_txt| 9; 10["salmonKallistoMtxTo10x"]; 7 -->|quants_mat_rows_txt| 10; 7 -->|quants_mat_cols_txt| 10; 7 -->|quants_mat_mtx| 10; 11["Join two Datasets"]; 10 -->|genes_out| 11; 5 -->|feature_annotation| 11; 12["Annotated Gene Table"]; 11 -->|out_file1| 12; 13["DropletUtils Read10x"]; 10 -->|barcodes_out| 13; 12 -->|out_file1| 13; 10 -->|matrix_out| 13; 14["DropletUtils emptyDrops"]; 13 -->|output_rds| 14; 68411264-f6f7-4e38-9a83-de6df68bd01d["Output\nEmptied-Object"]; 14 --> 68411264-f6f7-4e38-9a83-de6df68bd01d; style 68411264-f6f7-4e38-9a83-de6df68bd01d stroke:#2c3143,stroke-width:4px; 7a1fd602-7564-43b9-9cf4-bb84f4cc7cce["Output\nEmptied-Tabular Output"]; 14 --> 7a1fd602-7564-43b9-9cf4-bb84f4cc7cce; style 7a1fd602-7564-43b9-9cf4-bb84f4cc7cce stroke:#2c3143,stroke-width:4px; 15["N701-400k-AnnData"]; 14 -->|output_rdata| 15; 95846470-be60-462a-8660-d46eedff7746["Output\nN701-400k-AnnData"]; 15 --> 95846470-be60-462a-8660-d46eedff7746; style 95846470-be60-462a-8660-d46eedff7746 stroke:#2c3143,stroke-width:4px;
CS1_Generating a single cell matrix using Alevin
Wendi Bacon
Last updated Nov 12, 2022
Launch in Tutorial Mode
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated
flowchart TD 0["ℹ️ Input Dataset\nRead 1 - containing cell barcode & UMI"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nRead 2 - containing transcript"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nMus_musculus.GRCm38.cdna.all.fa"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nMus_musculus.GRCm38.100.gtf.gz"]; style 3 stroke:#2c3143,stroke-width:4px; 4["Transcript-gene mapping"]; 2 -->|output| 4; 3 -->|output| 4; 5["Gene information"]; 3 -->|output| 5; 6["Alevin Processed"]; 0 -->|output| 6; 1 -->|output| 6; 4 -->|fasta_output| 6; 4 -->|feature_annotation| 6; 7["Alevin - no processing"]; 0 -->|output| 7; 1 -->|output| 7; 4 -->|fasta_output| 7; 4 -->|feature_annotation| 7; 8["Droplet rank plot - Alevin barcodes"]; 6 -->|quants_mat_mtx| 8; 9["Droplet rank plot - raw barcodes"]; 6 -->|raw_cb_frequency_txt| 9; 10["salmonKallistoMtxTo10x"]; 7 -->|quants_mat_rows_txt| 10; 7 -->|quants_mat_cols_txt| 10; 7 -->|quants_mat_mtx| 10; 11["Join two Datasets"]; 10 -->|genes_out| 11; 5 -->|feature_annotation| 11; 12["Annotated Gene Table"]; 11 -->|out_file1| 12; 13["DropletUtils Read10x"]; 10 -->|barcodes_out| 13; 12 -->|out_file1| 13; 10 -->|matrix_out| 13; 14["DropletUtils emptyDrops"]; 13 -->|output_rds| 14; 8247429c-afeb-4640-94df-1d3f9eb261d9["Output\nStringent-Object"]; 14 --> 8247429c-afeb-4640-94df-1d3f9eb261d9; style 8247429c-afeb-4640-94df-1d3f9eb261d9 stroke:#2c3143,stroke-width:4px; 15["N701-400k-AnnData"]; 14 -->|output_rdata| 15; 95846470-be60-462a-8660-d46eedff7746["Output\nN701-400k-AnnData"]; 15 --> 95846470-be60-462a-8660-d46eedff7746; style 95846470-be60-462a-8660-d46eedff7746 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: