Workflows

These workflows are associated with Screening assembled genomes for contamination using NCBI FCS

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.

NCBI Foreign Contamination Screen
National Center for Biotechnology Information

Last updated Apr 16, 2024

Launch in Tutorial Mode
License: http://www.usa.gov/publicdomain/label/1.0/
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy France Galaxy Europe Galaxy Main Galaxy Australia Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nInput genome"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["FCS-GX screen"];
  0 -->|output| 1;
  9741edf2-4be6-45a3-980d-99b1aea18380["Output\nfcs_gx_action_report"];
  1 --> 9741edf2-4be6-45a3-980d-99b1aea18380;
  style 9741edf2-4be6-45a3-980d-99b1aea18380 stroke:#2c3143,stroke-width:4px;
  ddedd49f-8c57-4e3e-a158-3d66ce12f05c["Output\nfcs_gx_taxonomy_report"];
  1 --> ddedd49f-8c57-4e3e-a158-3d66ce12f05c;
  style ddedd49f-8c57-4e3e-a158-3d66ce12f05c stroke:#2c3143,stroke-width:4px;
  2["FCS-GX clean"];
  1 -->|action_report| 2;
  0 -->|output| 2;
  f3a37b43-d304-4ec0-a023-197c9e0ce2e1["Output\ngx_contam_fasta"];
  2 --> f3a37b43-d304-4ec0-a023-197c9e0ce2e1;
  style f3a37b43-d304-4ec0-a023-197c9e0ce2e1 stroke:#2c3143,stroke-width:4px;
  56716c7c-ac7f-42f7-bbef-62a36b4d3810["Output\ngx_clean_fasta"];
  2 --> 56716c7c-ac7f-42f7-bbef-62a36b4d3810;
  style 56716c7c-ac7f-42f7-bbef-62a36b4d3810 stroke:#2c3143,stroke-width:4px;
  3["FCS-adaptor screen"];
  2 -->|clean_fasta| 3;
  6a4baf46-80b0-4a96-b864-9201fc80cdb7["Output\nfcs_adaptor_report"];
  3 --> 6a4baf46-80b0-4a96-b864-9201fc80cdb7;
  style 6a4baf46-80b0-4a96-b864-9201fc80cdb7 stroke:#2c3143,stroke-width:4px;
  1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb["Output\nadaptor_clean_fasta"];
  3 --> 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb;
  style 1cad7ab4-a817-436c-9a63-fd4e3c6b4bbb stroke:#2c3143,stroke-width:4px;
  4["FCS-adaptor clean"];
  3 -->|adaptor_report| 4;
  2 -->|clean_fasta| 4;
  0da68570-7490-4087-86c8-739522e1a776["Output\nadaptor_contam_fasta"];
  4 --> 0da68570-7490-4087-86c8-739522e1a776;
  style 0da68570-7490-4087-86c8-739522e1a776 stroke:#2c3143,stroke-width:4px;
  4985eb07-30b0-4872-ab83-52ffeb619900["Output\nfinal_clean_fasta"];
  4 --> 4985eb07-30b0-4872-ab83-52ffeb619900;
  style 4985eb07-30b0-4872-ab83-52ffeb619900 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