Checking expected species and contamination in bacterial isolate

ecology-bacterial-isolate-species-contamination-checking/checking-expected-species-and-contamination-in-bacterial-isolate

Author(s)
Pierre, Bérénice Batut
Version
2
Last updated
Apr 4, 2024
License
GPL-3.0-or-later
Tags
ecology

Features
Tutorial
Checking expected species and contamination in bacterial isolate
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00044
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
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;

Inputs

Input Label
Input dataset reverse_reads
Input dataset forward_reads

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 Kraken2
toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0 Bracken
toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0 Recentrifuge

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/recentrifuge/recentrifuge/1.12.1+galaxy0 View in ToolShed

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

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

Version History

Version Commit Time Comments
3 4854483da 2024-04-04 12:32:05 Update Bracken version toolshed
2 96c80b0ad 2024-01-29 15:42:16 Update workflow creators
1 96df58f86 2024-01-29 15:33:59 Create new tutorial for checking expected species and contamination in bacterial isolate

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