Gene-based Pathogen Identification

microbiome-pathogen-detection-from-nanopore-foodborne-data/gene-based-pathogen-identification

Author(s)
Engy Nasr, Bérénice Batut, Paul Zierep
Version
2
Last updated
Jun 7, 2024
License
MIT
Tags
name:Collection
name:PathoGFAIR
name:IWC
name:microGalaxy

Features
Tutorial
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00142
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
list_output_txt
consensus
output
assembly_gfa
text_param
out_consensus
out_consensus
out_consensus
out1
output
out1
report
out1
report
outfile
ℹ️ Input Collection
collection_of_preprocessed_samples
Extract element identifiers
Build list
Split file
Flye
Parse parameter value
medaka consensus pipeline
Bandage Image
Compose text parameter value
FASTA-to-Tabular
ABRicate
ABRicate
Replace
Replace
Replace
Tabular-to-FASTA
Output
extracted_samples_IDs
Output
list_of_lists_of_preprocessed_samples
Output
splitted_extracted_samples_IDs
Output
flye_consensus_fasta
Output
flye_assembly_graph
Output
flye_assembly_gfa
Output
flye_assembly_info_tabular
Output
parsed_extracted_samples_IDs_to_text
Output
medaka_gaps_in_draft_bed_file
Output
medaka_log_file
Output
medaka_propability_h5_file
Output
medaka_calls_of_draft_bam_file
Output
sample_all_contigs
Output
bandage_assembly_graph_image
Output
sample_specific_contigs_tabular_file_preparation
Output
abricate_with_vfdb_to_identify_genes_with_VFs
Output
abricate_report_using_ncbi_database_to_indentify_amr
Output
sample_specific_contigs_tabular_file
Output
vfs
Output
amrs
Output
contigs

Inputs

Input Label
Input dataset collection collection_of_preprocessed_samples

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 Extract element identifiers
__BUILD_LIST__ Build list
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 Split file
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 Flye
param_value_from_file Parse parameter value
toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+galaxy0 medaka consensus pipeline
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 Bandage Image
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 FASTA-to-Tabular
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 ABRicate
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 ABRicate
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 Replace
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 Replace
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 Replace
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 Tabular-to-FASTA

Tools

Tool Links
__BUILD_LIST__
param_value_from_file
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.9.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/2022.09+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/medaka_consensus_pipeline/medaka_consensus_pipeline/1.7.2+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
2 cdd93376a 2024-06-06 12:00:29 adding tags to some of the workflow outputs, updating the training with the latest PathoGFAIR workflows updates
1 c63ce23c7 2024-05-26 12:29:47 updating workflows file names

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/pathogen-detection-from-nanopore-foodborne-data/workflows/gene_based_pathogen_identification.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