These workflows are associated with Genome annotation with Funannotate

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.

Anthony Bretaudeau

Last updated Apr 26, 2023

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

flowchart TD
  0["ℹ️ Input Dataset\nGenome assembly"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nRNASeq reads forward"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nRNASeq reads reverse"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nProtein evidence sequences"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nNCBI submission template"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\nAlternate annotation gbk"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\nAlternate annotation gff3"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["RNA STAR"];
  0 -->|output| 7;
  1 -->|output| 7;
  2 -->|output| 7;
  79cf59ea-3aef-4cb8-9c70-5b42e03a5da9["Output\nMapped RNASeq"];
  7 --> 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9;
  style 79cf59ea-3aef-4cb8-9c70-5b42e03a5da9 stroke:#2c3143,stroke-width:4px;
  8["Funannotate predict annotation"];
  3 -->|output| 8;
  7 -->|mapped_reads| 8;
  0 -->|output| 8;
  9["eggNOG Mapper"];
  8 -->|fasta_proteins| 9;
  8 -->|fasta_proteins| 10;
  11["Funannotate functional"];
  9 -->|annotations| 11;
  8 -->|annot_gbk| 11;
  10 -->|outfile_xml| 11;
  4 -->|output| 11;
  d0694cd1-6d81-4d72-83b9-94cb57dc1502["Output\nFinal annotation (genbank)"];
  11 --> d0694cd1-6d81-4d72-83b9-94cb57dc1502;
  style d0694cd1-6d81-4d72-83b9-94cb57dc1502 stroke:#2c3143,stroke-width:4px;
  9a1e7b70-1090-41ed-8637-65b7372a9f6c["Output\nFinal annotation (CDS sequences)"];
  11 --> 9a1e7b70-1090-41ed-8637-65b7372a9f6c;
  style 9a1e7b70-1090-41ed-8637-65b7372a9f6c stroke:#2c3143,stroke-width:4px;
  99fffa40-2196-491d-9a66-559ebf2d9561["Output\nFinal annotation (mRNA sequences)"];
  11 --> 99fffa40-2196-491d-9a66-559ebf2d9561;
  style 99fffa40-2196-491d-9a66-559ebf2d9561 stroke:#2c3143,stroke-width:4px;
  17b03b77-0485-4176-b2b3-03bfa2d3bcb0["Output\nFinal annotation (protein sequences)"];
  11 --> 17b03b77-0485-4176-b2b3-03bfa2d3bcb0;
  style 17b03b77-0485-4176-b2b3-03bfa2d3bcb0 stroke:#2c3143,stroke-width:4px;
  4a0602fc-e6d2-43fc-9957-344707c22c05["Output\nFinal annotation (GFF3)"];
  11 --> 4a0602fc-e6d2-43fc-9957-344707c22c05;
  style 4a0602fc-e6d2-43fc-9957-344707c22c05 stroke:#2c3143,stroke-width:4px;
  0 -->|output| 12;
  11 -->|gff3| 12;
  7 -->|mapped_reads| 12;
  12 --> ac4d8805-f123-44d2-b30f-8ac906cc471f;
  style ac4d8805-f123-44d2-b30f-8ac906cc471f stroke:#2c3143,stroke-width:4px;
  13["Funannotate compare"];
  5 -->|output| 13;
  11 -->|gbk| 13;
  e531c81f-f6b7-4c82-a712-c562873ff714["Output\nFunannotate compare report"];
  13 --> e531c81f-f6b7-4c82-a712-c562873ff714;
  style e531c81f-f6b7-4c82-a712-c562873ff714 stroke:#2c3143,stroke-width:4px;
  14["AEGeAn ParsEval"];
  6 -->|output| 14;
  11 -->|gff3| 14;
  0d776b46-2c1c-4083-9f9d-a213fa62eb81["Output\nAEGeAN report"];
  14 --> 0d776b46-2c1c-4083-9f9d-a213fa62eb81;
  style 0d776b46-2c1c-4083-9f9d-a213fa62eb81 stroke:#2c3143,stroke-width:4px;
  11 -->|fa_proteins| 15;
  57a619f5-b331-4ca6-8e6e-72eb61860032["Output\nBusco summary"];
  15 --> 57a619f5-b331-4ca6-8e6e-72eb61860032;
  style 57a619f5-b331-4ca6-8e6e-72eb61860032 stroke:#2c3143,stroke-width:4px;
  97d23764-ad4a-4d69-948c-c81afb76fbaf["Output\nBusco image"];
  15 --> 97d23764-ad4a-4d69-948c-c81afb76fbaf;
  style 97d23764-ad4a-4d69-948c-c81afb76fbaf 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: