Assembly-decontamination-VGP9

assembly-assembly-decontamination/main-workflow

Author(s)
Nadolina Brajuka
Version
1
Last updated
Sep 4, 2024
License
BSD-3-Clause
Tags
VGP_curated

Features
Tutorial
Decontamination of a genome assembly
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00284
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
outfile
output
output
output
output
output1
out_file1
out_file1
mito_scaff_names
out_file1
output
out_file1
ℹ️ Input Dataset
Scaffolded assembly fasta
ℹ️ Input Parameter
Database for Kraken2
soft-masking
hard-masking
ID non-target contaminants
blast mitochondria DB
Cut
parsing blast output
Filter
Cut
concatenate scaffold lists
removing scaffolds
Output
Kraken2 classification scores
Output
mito_scaff_names
Output
contaminants_table
Output
full contaminant + mito scaffold list
Output
final decontaminated assembly

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

Tool Links
Cut1
Filter1
toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.14.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_dustmasker_wrapper/2.14.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast/parse_mito_blast/1.0.2+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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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