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Add workflow for metagenomic taxonomic community profiling #1063

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d305446
Init metagenomic taxonomy analysis wf based on @Minamehr commit
bebatut Jan 15, 2026
737978b
Enhance workflow clarity, testing, and infrastructure
bebatut Jan 15, 2026
6d21ed6
Smaller test data and collection size conditioned subworkflows
bebatut Jan 20, 2026
af0de37
Add steps to prepare sylph output for MultiQC
bebatut Jan 21, 2026
995acd4
Try fix failing test with quoting ncbi taxonomy
bebatut Jan 21, 2026
00c3738
Update tools and apply copilot suggestions
bebatut Jan 21, 2026
1f18f91
Use smaller kraken/bracken databases
bebatut Jan 23, 2026
d0c3c0c
Use smallest ref db and try to fix tests
bebatut Jan 27, 2026
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15 changes: 15 additions & 0 deletions workflows/microbiome/metagenomic-taxonomic-community-profiling/.dockstore.yml
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version: 1.2
workflows:
- name: main
subclass: Galaxy
publish: true
primaryDescriptorPath: /metagenomic-taxonomic-community-profiling.ga
testParameterFiles:
- /metagenomic-taxonomic-community-profiling-tests.yml
authors:
- name: "B\xE9r\xE9nice Batut"
orcid: 0000-0001-9852-1987
- name: "G\xE9raldine Piot"
- name: Mina Hojat Ansari
orcid: 0000-0002-3602-7884
- name: AuBi (Auvergne Bioinformatique)
6 changes: 6 additions & 0 deletions workflows/microbiome/metagenomic-taxonomic-community-profiling/CHANGELOG.md
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# Changelog


## [0.1] - 2026-01-15

- First release
29 changes: 29 additions & 0 deletions workflows/microbiome/metagenomic-taxonomic-community-profiling/README.md
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# Metagenomic Community Profiling

This workflow performs taxonomic profiling on metagenomic short-read quality-controlled and host/contaminant removed data using multiple state-of-the-art tools, standardizes the generated outputs, and generates visualizations.

## Inputs

- Paired collection of **FastQ files** containing **metagenomic short-read data** after quality control and host/contamination removal
- **Reference databases** for the different taxonomy profiling tools

## Workflow Overview

1. **Taxonomy Profiling** using

- **Kraken2** (k-mer approach) with abundance re-estimation with **Bracken**
- **MetaPhlAn** (marker-based approach)
- **sylph** (k-mer approach)

2. **Standardization** of Kraken2/Bracken and MetaPhlAn outputs using **TaxPasta**

3. **Visualization** using
- **Krona** to generate interactive, hierarchical plots for exploring taxonomy profiles.
- **MultiQC** for aggregated HTML report for cross-sample and cross-tools comparisons

## Outputs

- Taxonomic profiles (Kraken2, Kraken2 + Bracken, MetaPhlAn, sylph)
- Standardized taxonomy tables (TaxPasta)
- Krona interactive plots
- MultiQC HTML report
320 changes: 320 additions & 0 deletions ...genomic-taxonomic-community-profiling/metagenomic-taxonomic-community-profiling-tests.yml
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- doc: Test with 1 sample for Metagenomics Taxonomic Community Profiling workflow
job:
Metagenomics Reads after Quality Control and Host/Contamination Removal:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: PSM6XBT3_500k
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17895994/files/PSM6XBT3_500k_R1.fastq.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/17895994/files/PSM6XBT3_500k_R2.fastq.gz
Reference Taxonomy Database for Kraken2: k2_minusb_20210517
Reference Taxonomy Database for Bracken: k2_minusb_20210517
Taxonomic Level for Abundance Re-estimation for Bracken: S
Reference Taxonomy Database for MetaPhlAn: mpa_vJan21_TOY_CHOCOPhlAnSGB_202103
Reference Database for Sylph: sylph_downloaded_12122025_OceanDNA-c200-v0.3.syldb
Reference Taxonomy Metadata for Sylph: sylph_tax_downloaded_08112025
NCBI Taxonomy for taxpasta: "2024-06-05"
outputs:
Kraken2 taxonomic profile:
element_tests:
PSM6XBT3_500k:
asserts:
has_n_lines:
n: 356
has_n_columns:
n: 6
has_text_matching:
expression: "Faecalibacterium virus Brigit"
has_text_matching:
expression: "D1"
MetaPhlAn taxonomy profile:
element_tests:
PSM6XBT3_500k:
asserts:
has_n_lines:
n: 22
has_text_matching:
expression: "#clade_name"
has_text_matching:
expression: "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Phocaeicola|s__Phocaeicola_vulgatus|t__SGB1814"
has_text_matching:
expression: "2|976|200643|171549||909656|821|"
Sylph taxonomy profile:
element_tests:
PSM6XBT3_500k:
asserts:
has_n_lines:
n: 9
has_n_columns:
n: 2
has_text_matching:
expression: "d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia flexneri"
has_text_matching:
expression: "PSM6XBT3_500k"
Bracken report:
element_tests:
PSM6XBT3_500k:
asserts:
has_n_lines:
n: 21
has_text_matching:
expression: "Faecalibacterium virus Brigit"
has_text_matching:
expression: "fraction_total_reads"
Standardized Kraken2/Bracken taxonomy profile:
asserts:
has_n_lines:
n: 21
has_n_columns:
n: 4
has_text_matching:
expression: "PSM6XBT3_500k"
has_text_matching:
expression: "Escherichia coli"
Standardized MetaPhlAn taxonomy profile:
asserts:
has_n_lines:
n: 14
has_n_columns:
n: 4
has_text_matching:
expression: "PSM6XBT3_500k"
has_text_matching:
expression: "Phocaeicola"
Krona chart for Kraken2 community profile:
asserts:
has_text_matching:
expression: "Bacteria"
has_text_matching:
expression: "Escherichia coli"
Krona chart for MetaPhlAn community profile:
asserts:
has_text_matching:
expression: "Root"
has_text_matching:
expression: "Phocaeicola"
Krona chart for Sylph community profile:
asserts:
has_text_matching:
expression: "Root"
has_text_matching:
expression: "Escherichia flexneri"
Krona chart for Kraken2/Bracken community profile:
asserts:
has_text_matching:
expression: "Root"
has_text_matching:
expression: "Faecalibacterium virus Brigit"
MultiQC HTML report:
asserts:
has_text_matching:
expression: "MetaPhlAn"
has_text_matching:
expression: "Kraken2"
has_text_matching:
expression: "Sylph"
has_text_matching:
expression: "Bracken"
has_text_matching:
expression: "Standardized"
- doc: Test with 2 samples for Metagenomics Taxonomic Community Profiling workflow
job:
Metagenomics Reads after Quality Control and Host/Contamination Removal:
class: Collection
collection_type: list:paired
elements:
- class: Collection
type: paired
identifier: PSM6XBT3_500k
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17895994/files/PSM6XBT3_500k_R1.fastq.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/17895994/files/PSM6XBT3_500k_R2.fastq.gz
- class: Collection
type: paired
identifier: PSM6XBT3_500k_2
elements:
- class: File
identifier: forward
location: https://zenodo.org/records/17895994/files/PSM6XBT3_500k_R1.fastq.gz
- class: File
identifier: reverse
location: https://zenodo.org/records/17895994/files/PSM6XBT3_500k_R2.fastq.gz
Reference Taxonomy Database for Kraken2: k2_minusb_20210517
Reference Taxonomy Database for Bracken: k2_minusb_20210517
Taxonomic Level for Abundance Re-estimation for Bracken: S
Reference Taxonomy Database for MetaPhlAn: mpa_vJan21_TOY_CHOCOPhlAnSGB_202103
Reference Database for Sylph: sylph_downloaded_12122025_OceanDNA-c200-v0.3.syldb
Reference Taxonomy Metadata for Sylph: sylph_tax_downloaded_08112025
NCBI Taxonomy for taxpasta: "2024-06-05"
outputs:
Kraken2 taxonomic profile:
element_tests:
PSM6XBT3_500k:
asserts:
has_n_lines:
n: 356
has_n_columns:
n: 6
has_text_matching:
expression: "Faecalibacterium virus Brigit"
has_text_matching:
expression: "D1"
PSM6XBT3_500k_2:
asserts:
has_n_lines:
n: 356
has_n_columns:
n: 6
has_text_matching:
expression: "Faecalibacterium virus Brigit"
has_text_matching:
expression: "D1"
MetaPhlAn taxonomy profile:
element_tests:
PSM6XBT3_500k:
asserts:
has_n_lines:
n: 22
has_text_matching:
expression: "#clade_name"
has_text_matching:
expression: "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Phocaeicola|s__Phocaeicola_vulgatus|t__SGB1814"
has_text_matching:
expression: "2|976|200643|171549||909656|821|"
PSM6XBT3_500k_2:
asserts:
has_n_lines:
n: 22
has_text_matching:
expression: "#clade_name"
has_text_matching:
expression: "k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_unclassified|g__Phocaeicola|s__Phocaeicola_vulgatus|t__SGB1814"
has_text_matching:
expression: "2|976|200643|171549||909656|821|"
Sylph taxonomy profile:
element_tests:
PSM6XBT3_500k:
asserts:
has_n_lines:
n: 9
has_n_columns:
n: 2
has_text_matching:
expression: "d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia flexneri"
has_text_matching:
expression: "PSM6XBT3_500k"
PSM6XBT3_500k_2:
asserts:
has_n_lines:
n: 9
has_n_columns:
n: 2
has_text_matching:
expression: "d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia flexneri"
has_text_matching:
expression: "PSM6XBT3_500k"
Bracken report:
element_tests:
PSM6XBT3_500k:
asserts:
has_n_lines:
n: 21
has_text_matching:
expression: "Faecalibacterium virus Brigit"
has_text_matching:
expression: "fraction_total_reads"
PSM6XBT3_500k_2:
asserts:
has_n_lines:
n: 21
has_text_matching:
expression: "Faecalibacterium virus Brigit"
has_text_matching:
expression: "fraction_total_reads"
Standardized Kraken2/Bracken taxonomy profile:
asserts:
has_n_lines:
n: 51
has_n_columns:
n: 5
has_text_matching:
expression: "PSM6XBT3_500k"
has_text_matching:
expression: "PSM6XBT3_500k_2"
has_text_matching:
expression: "Escherichia coli"
Standardized MetaPhlAn taxonomy profile:
asserts:
has_n_lines:
n: 21
has_n_columns:
n: 5
has_text_matching:
expression: "PSM6XBT3_500k"
has_text_matching:
expression: "PSM6XBT3_500k_2"
has_text_matching:
expression: "Phocaeicola"
Krona chart for Kraken2 community profile:
asserts:
has_text_matching:
expression: "Bacteria"
has_text_matching:
expression: "Proteobacteria"
Krona chart for MetaPhlAn community profile:
asserts:
has_text_matching:
expression: "Root"
has_text_matching:
expression: "Phocaeicola"
has_text_matching:
expression: "PSM6XBT3_500k"
has_text_matching:
expression: "PSM6XBT3_500k_2"
Krona chart for Sylph community profile:
asserts:
has_text_matching:
expression: "Root"
has_text_matching:
expression: "Escherichia flexneri"
has_text_matching:
expression: "PSM6XBT3_500k"
has_text_matching:
expression: "PSM6XBT3_500k_2"
Krona chart for Kraken2/Bracken community profile:
asserts:
has_text_matching:
expression: "Root"
has_text_matching:
expression: "Escherichia coli"
has_text_matching:
expression: "PSM6XBT3_500k"
has_text_matching:
expression: "PSM6XBT3_500k_2"
MultiQC HTML report:
asserts:
has_text_matching:
expression: "MetaPhlAn"
has_text_matching:
expression: "Kraken2"
has_text_matching:
expression: "Sylph"
has_text_matching:
expression: "Bracken"
has_text_matching:
expression: "Standardized"
has_text_matching:
expression: "PSM6XBT3_500k"
has_text_matching:
expression: "PSM6XBT3_500k_2"
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