MGnify's amplicon pipeline v5.0 - rRNA prediction

microbiome-mgnify-amplicon/mgnify-amplicon-pipeline-v5-rrna-prediction

Author(s)
EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep
version Version
1
last_modification Last updated
Jul 30, 2025
license License
Apache-2.0
galaxy-tags Tags
MGnify_Amplicon
metagenomics
amplicon
name:microgalaxy

Features
Tutorial
hands_on MGnify v5.0 Amplicon Pipeline
workflow Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
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Inputs

Input Label
Input dataset collection Processed sequences
Input dataset Clan information file

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1 Concatenate
toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2 FASTA Width
toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2 FASTA Width
__FILTER_EMPTY_DATASETS__ Filter empty datasets
__FILTER_EMPTY_DATASETS__ Filter empty datasets
__FILTER_EMPTY_DATASETS__ Filter empty datasets
__FILTER_EMPTY_DATASETS__ Filter empty datasets
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 Krona pie chart Krona SSU SILVA
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 Krona pie chart Krona LSU SILVA
toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1 Convert HDF5 SSU SILVA
toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1 Convert JSON SSU SILVA
toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1 Convert HDF5 LSU SILVA
toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1 Convert JSON LSU SILVA

Tools

Tool Links
__FILTER_EMPTY_DATASETS__
__FILTER_FROM_FILE__
param_value_from_file
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1 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/mapseq/mapseq/2.1.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy2 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
  1. Click on galaxy-workflows-activity 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 galaxy-upload 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
1 0125a7f84 2025-07-30 12:59:47 remove version from folder name for future-proofness

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/mgnify-amplicon/workflows/mgnify-amplicon-pipeline-v5-rrna-prediction.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