Workflows

These workflows are associated with An Introduction to 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.

Intro to Genome Assembly

Last updated Jul 25, 2020

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nmutant_R1.fastq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nmutant_R2.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nwildtype.fna"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["FastQC"];
  0 -->|output| 3;
  22a51e6e-2e5f-4415-a127-e0b1c179a1b1["Output\nfastqc_html"];
  3 --> 22a51e6e-2e5f-4415-a127-e0b1c179a1b1;
  style 22a51e6e-2e5f-4415-a127-e0b1c179a1b1 stroke:#2c3143,stroke-width:4px;
  51ec8c05-eb47-4359-9120-0eca1a6d5c2f["Output\nfastqc_txt"];
  3 --> 51ec8c05-eb47-4359-9120-0eca1a6d5c2f;
  style 51ec8c05-eb47-4359-9120-0eca1a6d5c2f stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  1 -->|output| 4;
  5["FASTQ interlacer"];
  0 -->|output| 5;
  1 -->|output| 5;
  225edf5f-3b90-4f84-a38a-5c786000a3fc["Output\noutput_pairs"];
  5 --> 225edf5f-3b90-4f84-a38a-5c786000a3fc;
  style 225edf5f-3b90-4f84-a38a-5c786000a3fc stroke:#2c3143,stroke-width:4px;
  dae90093-ae96-4bb2-824d-c92b61585096["Output\noutput_singles"];
  5 --> dae90093-ae96-4bb2-824d-c92b61585096;
  style dae90093-ae96-4bb2-824d-c92b61585096 stroke:#2c3143,stroke-width:4px;
  6["MultiQC"];
  3 -->|text_file| 6;
  4 -->|text_file| 6;
  85e3704a-859d-4657-b3d7-9b67e4981d21["Output\nmultiqc_stats"];
  6 --> 85e3704a-859d-4657-b3d7-9b67e4981d21;
  style 85e3704a-859d-4657-b3d7-9b67e4981d21 stroke:#2c3143,stroke-width:4px;
  fab7e06a-604e-4432-b0ed-b63157a8643b["Output\nmultiqc_report"];
  6 --> fab7e06a-604e-4432-b0ed-b63157a8643b;
  style fab7e06a-604e-4432-b0ed-b63157a8643b stroke:#2c3143,stroke-width:4px;
  7["velveth"];
  5 -->|outfile_pairs| 7;
  607a214d-9137-4e73-9b73-954c79678937["Output\nvelveth_out"];
  7 --> 607a214d-9137-4e73-9b73-954c79678937;
  style 607a214d-9137-4e73-9b73-954c79678937 stroke:#2c3143,stroke-width:4px;
  8["velvetg"];
  7 -->|out_file1| 8;
  b0cf3779-6199-42c9-963f-a733559f90bb["Output\nvelvet_contigs"];
  8 --> b0cf3779-6199-42c9-963f-a733559f90bb;
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  54926701-ccae-4143-b649-b7e08e1c6a8e["Output\nvelvet_stats"];
  8 --> 54926701-ccae-4143-b649-b7e08e1c6a8e;
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  9["Quast"];
  2 -->|output| 9;
  8 -->|contigs| 9;
  0babe959-4d63-4838-9e18-4526b3dd0db5["Output\nquast_report_html"];
  9 --> 0babe959-4d63-4838-9e18-4526b3dd0db5;
  style 0babe959-4d63-4838-9e18-4526b3dd0db5 stroke:#2c3143,stroke-width:4px;
  f41c43c4-763c-42bc-b36e-9ea76e7752c2["Output\nquast_report_pdf"];
  9 --> f41c43c4-763c-42bc-b36e-9ea76e7752c2;
  style f41c43c4-763c-42bc-b36e-9ea76e7752c2 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:

Video: Importing a workflow from URL