Nanopore Preprocessing

microbiome-pathogen-detection-from-nanopore-foodborne-data/nanopore-preprocessing

Author(s)
Bérénice Batut, Engy Nasr, Paul Zierep
Version
3
Last updated
Jun 7, 2024
License
MIT
Tags
name:Collection
name:microGalaxy
name:PathoGFAIR
name:Nanopore
name:IWC

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:W00143
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
outfile
text_file
output
out1
out1
out1
alignment_output
text_file
mapped
unmapped
out_file1
output
output
output
output
out1
report_output
output
text_file
out_file1
output
out_file1
out_file1
tabular_output
out_file1
text_file
out_file1
ℹ️ Input Parameter
samples_profile
ℹ️ Input Collection
collection_of_all_samples
Porechop
NanoPlot
FastQC
fastp
MultiQC
Map with minimap2
NanoPlot
FastQC
Split BAM by reads mapping status
Select
Samtools fastx
Samtools fastx
Collapse Collection
Filter failed datasets
Kraken2
Cut
FastQC
Krakentools: Extract Kraken Reads By ID
Select
Collapse Collection
Cut
Column join
Compute
Column Regex Find And Replace
MultiQC
Output
porechop_output_trimmed_reads
Output
nanoplot_qc_on_reads_before_preprocessing_nanostats
Output
nanoplot_on_reads_before_preprocessing_nanostats_post_filtering
Output
nanoplot_qc_on_reads_before_preprocessing_html_report
Output
fastqc_quality_check_before_preprocessing_html_file
Output
fastqc_quality_check_before_preprocessing_text_file
Output
nanopore_sequenced_reads_processed_with_fastp_after_host_removal
Output
nanopore_sequenced_reads_processed_with_fastp_after_host_removal_html_report
Output
multiQC_stats_before_preprocessing
Output
multiQC_html_report_before_preprocessing
Output
bam_map_to_host
Output
nanoplot_qc_on_reads_after_preprocessing_html_report
Output
nanoplot_on_reads_after_preprocessing_nanostats_post_filtering
Output
nanoplot_qc_on_reads_after_preprocessing_nanostats
Output
fastqc_quality_check_after_preprocessing_text_file
Output
fastqc_quality_check_after_preprocessing_html_file
Output
non_host_sequences_bam
Output
host_sequences_bam
Output
total_sequences_before_hosts_sequences_removal
Output
host_sequences_fastq
Output
non_host_sequences_fastq
Output
kraken2_with_kalamri_database_output
Output
kraken2_with_kalamri_database_report
Output
quality_retained_all_reads
Output
hosts_qc_text_file
Output
hosts_qc_html
Output
collection_of_preprocessed_samples
Output
total_sequences_after_hosts_sequences_removal
Output
quality_retained_hosts_reads
Output
removed_hosts_percentage_tabular
Output
multiQC_html_report_after_preprocessing
Output
multiQC_stats_after_preprocessing

Inputs

Input Label
Input parameter samples_profile
Input dataset collection collection_of_all_samples

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 Porechop
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1 NanoPlot
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 FastQC
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0 fastp
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 MultiQC
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0 Map with minimap2
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1 NanoPlot
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 FastQC
toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2 Split BAM by reads mapping status
Grep1 Select
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2 Samtools fastx
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2 Samtools fastx
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy1 Kraken2
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 FastQC
toolshed.g2.bx.psu.edu/repos/iuc/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1 Krakentools: Extract Kraken Reads By ID
Grep1 Select
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 Column Regex Find And Replace
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 MultiQC

Tools

Tool Links
Cut1
Grep1
__FILTER_FAILED_DATASETS__
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bamtools_split_mapped/bamtools_split_mapped/2.5.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+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/krakentools_extract_kraken_reads/krakentools_extract_kraken_reads/1.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.42.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.15.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 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
5 cdd93376a 2024-06-06 12:00:29 adding tags to some of the workflow outputs, updating the training with the latest PathoGFAIR workflows updates
4 e230001f4 2024-05-29 11:33:18 updating preprocessing workflow and allele based workflow with a single user input parameter and adjusting the md file accodingly
3 211b69394 2024-05-26 09:45:27 adding workflow reports to the workflows of the training to match the latest version of the IWC PR
2 d320748c5 2024-05-20 18:17:48 Foodborne training update 2024
1 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

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