Workflows

These workflows are associated with Checking expected species and contamination in bacterial isolate

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.

Checking expected species and contamination in bacterial isolate
Pierre, Bérénice Batut

Last updated Apr 4, 2024

Launch in Tutorial Mode
License: GPL-3.0-or-later
Tests: ✅ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Main Galaxy Australia Galaxy Europe Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nreverse_reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nforward_reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Kraken2"];
  1 -->|output| 2;
  0 -->|output| 2;
  a408a644-58cd-4f5e-af25-15b5ea63aa76["Output\nkraken_report_reads"];
  2 --> a408a644-58cd-4f5e-af25-15b5ea63aa76;
  style a408a644-58cd-4f5e-af25-15b5ea63aa76 stroke:#2c3143,stroke-width:4px;
  54b85a53-72ee-4b73-b186-7fd55e8aab9b["Output\nkraken_report_tabular"];
  2 --> 54b85a53-72ee-4b73-b186-7fd55e8aab9b;
  style 54b85a53-72ee-4b73-b186-7fd55e8aab9b stroke:#2c3143,stroke-width:4px;
  3["Bracken"];
  2 -->|report_output| 3;
  ae6c6464-f5f5-4e5b-b616-d38166fc0133["Output\nbracken_report_tsv"];
  3 --> ae6c6464-f5f5-4e5b-b616-d38166fc0133;
  style ae6c6464-f5f5-4e5b-b616-d38166fc0133 stroke:#2c3143,stroke-width:4px;
  8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8["Output\nbracken_kraken_report"];
  3 --> 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8;
  style 8ca52af9-f839-42b6-aa74-f1a6a1dfbbc8 stroke:#2c3143,stroke-width:4px;
  4["Recentrifuge"];
  2 -->|output| 4;
  b5694f2d-c8cd-4460-bfff-74fd0792ecb3["Output\nrecentrifuge_stats_tabular"];
  4 --> b5694f2d-c8cd-4460-bfff-74fd0792ecb3;
  style b5694f2d-c8cd-4460-bfff-74fd0792ecb3 stroke:#2c3143,stroke-width:4px;
  bd947a1d-0443-465f-8658-5d76d9ce69f8["Output\nrecentrifuge_report_html"];
  4 --> bd947a1d-0443-465f-8658-5d76d9ce69f8;
  style bd947a1d-0443-465f-8658-5d76d9ce69f8 stroke:#2c3143,stroke-width:4px;
  c7457acb-41bc-4191-b3fb-6716e15fbe57["Output\nrecentrifuge_data_tabular"];
  4 --> c7457acb-41bc-4191-b3fb-6716e15fbe57;
  style c7457acb-41bc-4191-b3fb-6716e15fbe57 stroke:#2c3143,stroke-width:4px;
  94f6ff07-0e06-47ad-88f8-a058d0808537["Output\nrecentrifuge_logfile"];
  4 --> 94f6ff07-0e06-47ad-88f8-a058d0808537;
  style 94f6ff07-0e06-47ad-88f8-a058d0808537 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: