Gigascience_Fusions_demonstration_STS26T-Gent_Workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nRNA-Seq_Reads_1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nRNA-Seq_Reads_2"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nhuman_reference_genome_annotation.gtf"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nhuman_reference_genome.fasta"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Arriba-Get-Filters"];
  bdb7b8fe-ad19-44b0-8824-c930809543eb["Output\nArriba-Get-Filters_protein_domains"];
  4 --> bdb7b8fe-ad19-44b0-8824-c930809543eb;
  style bdb7b8fe-ad19-44b0-8824-c930809543eb stroke:#2c3143,stroke-width:4px;
  d19553ea-c199-47b1-ad18-f7197de66fc7["Output\nArriba-Get-Filters_cytobands"];
  4 --> d19553ea-c199-47b1-ad18-f7197de66fc7;
  style d19553ea-c199-47b1-ad18-f7197de66fc7 stroke:#2c3143,stroke-width:4px;
  02a9718d-0153-4bf8-b7b9-17826109ede7["Output\nArriba-Get-Filters_blacklist"];
  4 --> 02a9718d-0153-4bf8-b7b9-17826109ede7;
  style 02a9718d-0153-4bf8-b7b9-17826109ede7 stroke:#2c3143,stroke-width:4px;
  75ae6bd6-5b30-4af1-bc91-2f2c798a44ef["Output\nArriba-Get-Filters_known_fusions"];
  4 --> 75ae6bd6-5b30-4af1-bc91-2f2c798a44ef;
  style 75ae6bd6-5b30-4af1-bc91-2f2c798a44ef stroke:#2c3143,stroke-width:4px;
  5["Uncompressed-RNA-Seq-forward-reads"];
  0 -->|output| 5;
  ad7de653-861f-4fe5-961b-0ec2bd2485dc["Output\nUncompressed-RNA-Seq-forward-reads"];
  5 --> ad7de653-861f-4fe5-961b-0ec2bd2485dc;
  style ad7de653-861f-4fe5-961b-0ec2bd2485dc stroke:#2c3143,stroke-width:4px;
  6["Uncompressed-RNA-Seq-reverse-reads"];
  1 -->|output| 6;
  30fe35ba-5af2-4f36-ab8a-7f0099253882["Output\nUncompressed-RNA-Seq-reverse-reads"];
  6 --> 30fe35ba-5af2-4f36-ab8a-7f0099253882;
  style 30fe35ba-5af2-4f36-ab8a-7f0099253882 stroke:#2c3143,stroke-width:4px;
  7["RNA_STAR"];
  2 -->|output| 7;
  5 -->|output1| 7;
  6 -->|output1| 7;
  8002eb14-9ce0-4767-8e64-ad5d8af17f25["Output\nRNA_STAR_mapped_reads"];
  7 --> 8002eb14-9ce0-4767-8e64-ad5d8af17f25;
  style 8002eb14-9ce0-4767-8e64-ad5d8af17f25 stroke:#2c3143,stroke-width:4px;
  8["Arriba"];
  4 -->|blacklist| 8;
  2 -->|output| 8;
  3 -->|output| 8;
  7 -->|mapped_reads| 8;
  4 -->|known_fusions| 8;
  4 -->|protein_domains| 8;
  4 -->|cytobands| 8;
  4cb6fdb6-b4c5-47b4-9dca-3a05a7a26c74["Output\nArriba-Fusions-tsv"];
  8 --> 4cb6fdb6-b4c5-47b4-9dca-3a05a7a26c74;
  style 4cb6fdb6-b4c5-47b4-9dca-3a05a7a26c74 stroke:#2c3143,stroke-width:4px;
  9["Reformating Fusion data"];
  8 -->|fusions_tsv| 9;
  a8817c07-800d-4588-8c87-18ab611f85a8["Output\nReformated_Fusion_data"];
  9 --> a8817c07-800d-4588-8c87-18ab611f85a8;
  style a8817c07-800d-4588-8c87-18ab611f85a8 stroke:#2c3143,stroke-width:4px;
  10["Table_generation_from_Fusion_data"];
  9 -->|outfile| 10;
  ab3ad7b0-6f43-4f0f-9e0f-758c721a03f0["Output\nTable_generation_from_Fusion_data"];
  10 --> ab3ad7b0-6f43-4f0f-9e0f-758c721a03f0;
  style ab3ad7b0-6f43-4f0f-9e0f-758c721a03f0 stroke:#2c3143,stroke-width:4px;
  11["Converting_Tabular_to_Fasta"];
  10 -->|output| 11;
  e21178f2-6a4a-4174-9660-1af15ff7dbb4["Output\nConverting_Tabular_to_Fasta"];
  11 --> e21178f2-6a4a-4174-9660-1af15ff7dbb4;
  style e21178f2-6a4a-4174-9660-1af15ff7dbb4 stroke:#2c3143,stroke-width:4px;
  12["Arriba-Fusion-Database"];
  11 -->|output| 12;
  be2983fd-4ddf-4593-8b8d-933393eac469["Output\nArriba-Fusion-Database"];
  12 --> be2983fd-4ddf-4593-8b8d-933393eac469;
  style be2983fd-4ddf-4593-8b8d-933393eac469 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/proteomics/tutorials/neoantigen-1-fusion-database-generation/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