Workflows
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.
Chloroplast-genome-assembly-and-annotation
Last updated May 10, 2023
Launch in Tutorial Mode
License:
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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; 5["NanoPlot"]; 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; 10["pilon"]; 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; 14["Prokka"]; 10 -->|output_fasta| 14; 15["JBrowse"]; 10 -->|output_fasta| 15; 12 -->|bam_output| 15; 13 -->|bam_output| 15; 16["JBrowse"]; 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: