Workflows

These workflows are associated with Bacterial Genome Annotation

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.

Bacterial Genome Annotation
Bérénice Batut, Pierre Marin

Last updated Jan 29, 2024

Launch in Tutorial Mode question
License: AGPL-3.0-or-later
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\ncontigs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ISEScan"];
  0 -->|output| 1;
  2bb672cb-4536-46b0-8a22-8590a0ca36c7["Output\nisescan_results"];
  1 --> 2bb672cb-4536-46b0-8a22-8590a0ca36c7;
  style 2bb672cb-4536-46b0-8a22-8590a0ca36c7 stroke:#2c3143,stroke-width:4px;
  2["PlasmidFinder"];
  0 -->|output| 2;
  614064e6-4b0f-4e38-b04e-e3f61ba41b46["Output\nplasmidfinder_results"];
  2 --> 614064e6-4b0f-4e38-b04e-e3f61ba41b46;
  style 614064e6-4b0f-4e38-b04e-e3f61ba41b46 stroke:#2c3143,stroke-width:4px;
  3["Integron Finder"];
  0 -->|output| 3;
  d26788cf-2441-4f29-ac39-b6be96f192eb["Output\nintegronfinder_summary"];
  3 --> d26788cf-2441-4f29-ac39-b6be96f192eb;
  style d26788cf-2441-4f29-ac39-b6be96f192eb stroke:#2c3143,stroke-width:4px;
  4["Bakta"];
  0 -->|output| 4;
  d3a40a8b-1bd1-42b6-a91e-756379b86d94["Output\nbakta_summary"];
  4 --> d3a40a8b-1bd1-42b6-a91e-756379b86d94;
  style d3a40a8b-1bd1-42b6-a91e-756379b86d94 stroke:#2c3143,stroke-width:4px;
  5["Group"];
  1 -->|all_results| 5;
  6["Group"];
  1 -->|all_results| 6;
  7["Replace Text"];
  2 -->|result_file| 7;
  8["Select last"];
  7 -->|outfile| 8;
  9["Table to GFF3"];
  8 -->|outfile| 9;
  10["JBrowse"];
  0 -->|output| 10;
  4 -->|annotation_gff3| 10;
  9 -->|output| 10;
  1 -->|annotation| 10;
	

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