MGnify's amplicon pipeline v5.0 - rRNA prediction
microbiome-mgnify-amplicon/mgnify-amplicon-pipeline-v5-rrna-prediction
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12 -->|output| 15; 16["Extract element identifiers"]; 13 -->|output| 16; 17["Filter collection"]; 15 -->|output| 17; 0 -->|output| 17; 18["Filter collection"]; 16 -->|output| 18; 0 -->|output| 18; 19["bedtools getfasta"]; 17 -->|output_filtered| 19; 12 -->|output| 19; 20["bedtools getfasta"]; 18 -->|output_filtered| 20; 13 -->|output| 20; 21["FASTA Width"]; 19 -->|output| 21; a5040877-43f1-4942-b2de-404c98bac842["Output\nSSU FASTA files"]; 21 --> a5040877-43f1-4942-b2de-404c98bac842; style a5040877-43f1-4942-b2de-404c98bac842 stroke:#2c3143,stroke-width:4px; 22["FASTA Width"]; 20 -->|output| 22; 2cc6ed90-b1f0-438f-8cfe-1a4877295079["Output\nLSU FASTA files"]; 22 --> 2cc6ed90-b1f0-438f-8cfe-1a4877295079; style 2cc6ed90-b1f0-438f-8cfe-1a4877295079 stroke:#2c3143,stroke-width:4px; 23["MAPseq"]; 21 -->|output| 23; 24["MAPseq"]; 22 -->|output| 24; 25["Text reformatting"]; 23 -->|classifications| 25; 26["Text reformatting"]; 23 -->|otu_tsv| 26; 27["Text reformatting"]; 23 -->|otu_tsv_notaxid| 27; 28["Filter empty datasets"]; 23 -->|krona_format| 28; 29["Text reformatting"]; 24 -->|classifications| 29; 30["Text reformatting"]; 24 -->|otu_tsv| 30; 31["Text reformatting"]; 24 -->|otu_tsv_notaxid| 31; 32["Filter empty datasets"]; 24 -->|krona_format| 32; 33["Filter empty datasets"]; 25 -->|outfile| 33; 2f42bcff-aeba-4628-9f36-d7f564b39de3["Output\nSSU taxonomic classifications using SILVA DB"]; 33 --> 2f42bcff-aeba-4628-9f36-d7f564b39de3; style 2f42bcff-aeba-4628-9f36-d7f564b39de3 stroke:#2c3143,stroke-width:4px; 34["Filter empty datasets"]; 26 -->|outfile| 34; 646eda6d-d954-40b7-a4f0-c4ce1346e239["Output\nSSU OTU tables (SILVA DB)"]; 34 --> 646eda6d-d954-40b7-a4f0-c4ce1346e239; style 646eda6d-d954-40b7-a4f0-c4ce1346e239 stroke:#2c3143,stroke-width:4px; 35["Filter empty datasets"]; 27 -->|outfile| 35; 36["🛠️ Subworkflow\nMap empty/not empty collection to boolean "]; style 36 fill:#edd,stroke:#900,stroke-width:4px; 28 -->|output| 36; 37["Filter empty datasets"]; 29 -->|outfile| 37; 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43 -->|boolean_param| 47; 48da1567-b17d-473f-96c1-d137073f6d12["Output\nLSU OTU tables in HDF5 format (SILVA DB)"]; 47 --> 48da1567-b17d-473f-96c1-d137073f6d12; style 48da1567-b17d-473f-96c1-d137073f6d12 stroke:#2c3143,stroke-width:4px; 48["JSON LSU SILVA"]; 39 -->|output| 48; 43 -->|boolean_param| 48; 5d5b34f6-6f44-4bad-bd38-ecb70ccc3451["Output\nLSU OTU tables in JSON format (SILVA DB)"]; 48 --> 5d5b34f6-6f44-4bad-bd38-ecb70ccc3451; style 5d5b34f6-6f44-4bad-bd38-ecb70ccc3451 stroke:#2c3143,stroke-width:4px;
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
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 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
- 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 |
---|---|---|---|
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