Workflow constructed from history 'Tuto Obitools'

ecology-Obitools-metabarcoding/main-workflow

Author(s)

version Version
1
last_modification Last updated
Feb 28, 2022
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
ecology

Features

Tutorial
hands_on Metabarcoding/eDNA through Obitools

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00042
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nwolf_tutorial.zip?download=1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Illuminapairedend"];
  2["Unzip"];
  0 -->|output| 2;
  3["FastQC"];
  1 -->|output| 3;
  4["FASTQ Groomer"];
  1 -->|output| 4;
  5["obigrep"];
  4 -->|output_file| 5;
  6["Line/Word/Character count"];
  4 -->|output_file| 6;
  7["Line/Word/Character count"];
  5 -->|output| 7;
  8["NGSfilter"];
  5 -->|output| 8;
  9["obiuniq"];
  8 -->|output| 9;
  10["obiannotate"];
  9 -->|output| 10;
  11["obistat"];
  10 -->|output| 11;
  12["obigrep"];
  10 -->|output| 12;
  13["obigrep"];
  12 -->|output| 13;
  14["obiclean"];
  13 -->|output| 14;
  15["NCBI BLAST+ blastn"];
  14 -->|output| 15;
  16["Filter sequences by ID"];
  15 -->|output1| 16;
  17["Filter sequences by ID"];
  15 -->|output1| 17;
  14 -->|output| 17;
  18["obitab"];
  16 -->|output_pos| 18;
  19["obitab"];
  17 -->|output_pos| 19;
  20["Join two Datasets"];
  19 -->|output| 20;
  15 -->|output1| 20;
  21["Join two Datasets"];
  20 -->|out_file1| 21;
  18 -->|output| 21;
  22["Cut"];
  21 -->|out_file1| 22;
  23["Filter"];
  22 -->|out_file1| 23;

Inputs

Input Label
Input dataset wolf_tutorial.zip?download=1

Outputs

From Output Label

Tools

Tool Links
Cut1
Filter1
join1
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13 View in ToolShed
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7 View in ToolShed
wc_gnu

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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
3 20d3c8cef 2022-02-25 09:32:05 fix workflow linting
2 931fb1735 2022-02-18 23:56:52 update workflow
1 45ca3bc6d 2022-01-31 20:10:46 Add files via upload

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/ecology/tutorials/Obitools-metabarcoding/workflows/main_workflow.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