Checking expected species and contamination in bacterial isolate

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Europe
• Galaxy Australia
• 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;

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.

Importing into Galaxy

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/ecology/tutorials/bacterial-isolate-species-contamination-checking/workflows/Checking-expected-species-and-contamination-in-bacterial-isolate.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows