Workflows

These workflows are associated with Assembly of the mitochondrial genome from PacBio HiFi reads

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.

Mitogenome-Assembly-VGP0
VGP, Galaxy

Last updated Sep 3, 2024

Launch in Tutorial Mode
License: CC-BY-4.0
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy France Galaxy Australia Galaxy Europe Galaxy Main Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Collection\nCollection of Pacbio Data"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nSpecies name latin name"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nEmail adress"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["MitoHiFi"];
  2 -->|output| 3;
  1 -->|output| 3;
  4["MitoHiFi"];
  0 -->|output| 4;
  3 -->|fasta_reference| 4;
  3 -->|genbank_reference| 4;
  31807e4b-e616-4742-92e0-934e6c3c09ae["Output\ncontigs_stats"];
  4 --> 31807e4b-e616-4742-92e0-934e6c3c09ae;
  style 31807e4b-e616-4742-92e0-934e6c3c09ae stroke:#2c3143,stroke-width:4px;
  8393c665-a328-4698-93e5-198c6fea52dd["Output\nmitogenome_coverage"];
  4 --> 8393c665-a328-4698-93e5-198c6fea52dd;
  style 8393c665-a328-4698-93e5-198c6fea52dd stroke:#2c3143,stroke-width:4px;
  85061673-df5e-480d-920a-a11c72bf8f56["Output\nmitogenome_annotation"];
  4 --> 85061673-df5e-480d-920a-a11c72bf8f56;
  style 85061673-df5e-480d-920a-a11c72bf8f56 stroke:#2c3143,stroke-width:4px;
  fe4d1d3d-9caa-45f6-944e-c4b101105dd1["Output\nmitogenome_genbank"];
  4 --> fe4d1d3d-9caa-45f6-944e-c4b101105dd1;
  style fe4d1d3d-9caa-45f6-944e-c4b101105dd1 stroke:#2c3143,stroke-width:4px;
  5["Compress files"];
  4 -->|mitogenome_fasta| 5;
  6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed["Output\noutput_file"];
  5 --> 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed;
  style 6f918a08-1ca1-4d6e-a4d8-7e65e13a65ed 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 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