Launch in Tutorial Mode
question
Run Workflow in Galaxy
galaxy-download
Download
flowchart TD
0["ℹ️ Input Dataset\nScaffolded assembly fasta"];
style 0 stroke:#2c3143,stroke-width:4px;
1["ℹ️ Input Parameter\nDatabase for Kraken2"];
style 1 fill:#ded,stroke:#393,stroke-width:4px;
2["soft-masking "];
0 -->|output| 2;
3["hard-masking"];
2 -->|outfile| 3;
4["ID non-target contaminants"];
1 -->|output| 4;
3 -->|output| 4;
c380857b-5180-4e82-a14f-8b575f10abaa["Output\nKraken2 classification scores"];
4 --> c380857b-5180-4e82-a14f-8b575f10abaa;
style c380857b-5180-4e82-a14f-8b575f10abaa stroke:#2c3143,stroke-width:4px;
5["blast mitochondria DB"];
3 -->|output| 5;
6["Cut"];
4 -->|output| 6;
7["parsing blast output"];
5 -->|output1| 7;
1478af1e-52f4-48fe-b966-0a61e2014a58["Output\nmito_scaff_names"];
7 --> 1478af1e-52f4-48fe-b966-0a61e2014a58;
style 1478af1e-52f4-48fe-b966-0a61e2014a58 stroke:#2c3143,stroke-width:4px;
8["Filter"];
6 -->|out_file1| 8;
64156e28-aaf0-4578-9a7e-d6d21774c2c8["Output\ncontaminants_table"];
8 --> 64156e28-aaf0-4578-9a7e-d6d21774c2c8;
style 64156e28-aaf0-4578-9a7e-d6d21774c2c8 stroke:#2c3143,stroke-width:4px;
9["Cut"];
8 -->|out_file1| 9;
10["concatenate scaffold lists"];
7 -->|mito_scaff_names| 10;
9 -->|out_file1| 10;
77084ec5-a145-40c1-9cfc-476d091105ae["Output\nfull contaminant + mito scaffold list"];
10 --> 77084ec5-a145-40c1-9cfc-476d091105ae;
style 77084ec5-a145-40c1-9cfc-476d091105ae stroke:#2c3143,stroke-width:4px;
11["removing scaffolds "];
0 -->|output| 11;
10 -->|out_file1| 11;
88a8e9ed-d92c-4340-aaad-c6d450a336aa["Output\nfinal decontaminated assembly"];
11 --> 88a8e9ed-d92c-4340-aaad-c6d450a336aa;
style 88a8e9ed-d92c-4340-aaad-c6d450a336aa stroke:#2c3143,stroke-width:4px;
Inputs
Input
Label
Input dataset
Scaffolded assembly (fasta)
Input parameter
Database for Kraken2
Outputs
From
Output
Label
Input parameter
Database for Kraken2
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1
Kraken2
ID non-target contaminants
toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+galaxy0
Parse mitochondrial blast
parsing blast output
Filter1
Filter
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1
Concatenate datasets
concatenate scaffold lists
toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0
gfastats
removing scaffolds
Tools
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
8508dbeac
2024-09-03 19:00:32
format workflow and update test to the latest version of the workflow
2
eb3c5175f
2024-08-23 20:55:43
Simplify the workflow
1
72a8cb1ed
2024-08-16 16:20:33
creation of a tutorial for Asssembly decontamination'
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-decontamination/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