These workflows are associated with Chloroplast genome assembly

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.


Last updated May 10, 2023

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Tests: ❌ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nIllumina_reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nNanopore_reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nTiny_set_illumina_read"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nTiny_set_nanopore_reads"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Flye assembly"];
  1 -->|output| 4;
  1 -->|output| 5;
  6["Map with BWA-MEM"];
  0 -->|output| 6;
  4 -->|consensus| 6;
  7["Fasta Statistics"];
  4 -->|consensus| 7;
  8["Bandage Info"];
  4 -->|assembly_gfa| 8;
  9["Bandage Image"];
  4 -->|assembly_gfa| 9;
  6 -->|bam_output| 10;
  4 -->|consensus| 10;
  11["Fasta Statistics"];
  10 -->|output_fasta| 11;
  12["Map with BWA-MEM"];
  2 -->|output| 12;
  10 -->|output_fasta| 12;
  13["Map with BWA-MEM"];
  3 -->|output| 13;
  10 -->|output_fasta| 13;
  10 -->|output_fasta| 14;
  10 -->|output_fasta| 15;
  12 -->|bam_output| 15;
  13 -->|bam_output| 15;
  10 -->|output_fasta| 16;
  14 -->|out_gff| 16;

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: