Workflows

These workflows are associated with Decontamination of a 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.

Assembly-decontamination-VGP9
Nadolina Brajuka

Last updated Sep 4, 2024

Launch in Tutorial Mode
License: BSD-3-Clause
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Europe Galaxy Australia Galaxy France Galaxy Main Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nScaffolded assembly fasta"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nDatabase for Kraken2"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["soft-masking "];
  0 -->|output| 2;
  3["hard-masking"];
  2 -->|outfile| 3;
  4["ID non-target contaminants"];
  1 -->|output| 4;
  3 -->|output| 4;
  c380857b-5180-4e82-a14f-8b575f10abaa["Output\nKraken2 classification scores"];
  4 --> c380857b-5180-4e82-a14f-8b575f10abaa;
  style c380857b-5180-4e82-a14f-8b575f10abaa stroke:#2c3143,stroke-width:4px;
  5["blast mitochondria DB"];
  3 -->|output| 5;
  6["Cut"];
  4 -->|output| 6;
  7["parsing blast output"];
  5 -->|output1| 7;
  1478af1e-52f4-48fe-b966-0a61e2014a58["Output\nmito_scaff_names"];
  7 --> 1478af1e-52f4-48fe-b966-0a61e2014a58;
  style 1478af1e-52f4-48fe-b966-0a61e2014a58 stroke:#2c3143,stroke-width:4px;
  8["Filter"];
  6 -->|out_file1| 8;
  64156e28-aaf0-4578-9a7e-d6d21774c2c8["Output\ncontaminants_table"];
  8 --> 64156e28-aaf0-4578-9a7e-d6d21774c2c8;
  style 64156e28-aaf0-4578-9a7e-d6d21774c2c8 stroke:#2c3143,stroke-width:4px;
  9["Cut"];
  8 -->|out_file1| 9;
  10["concatenate scaffold lists"];
  7 -->|mito_scaff_names| 10;
  9 -->|out_file1| 10;
  77084ec5-a145-40c1-9cfc-476d091105ae["Output\nfull contaminant + mito scaffold list"];
  10 --> 77084ec5-a145-40c1-9cfc-476d091105ae;
  style 77084ec5-a145-40c1-9cfc-476d091105ae stroke:#2c3143,stroke-width:4px;
  11["removing scaffolds "];
  0 -->|output| 11;
  10 -->|out_file1| 11;
  88a8e9ed-d92c-4340-aaad-c6d450a336aa["Output\nfinal decontaminated assembly"];
  11 --> 88a8e9ed-d92c-4340-aaad-c6d450a336aa;
  style 88a8e9ed-d92c-4340-aaad-c6d450a336aa 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