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 question
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 question
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: