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Merge pull request #995 from hugolefeuvre/genes_collection_metaG
Genes catalogue build workflow from metagenomic raw reads data
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‎workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml‎

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- hash_function: SHA-1
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hash_value: a3545f886ccca21cba986bf12daa2240f36ef1b6
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Select a taxonomy group point mutation: Enterococcus_faecalis
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Select a AMR genes detection database: amrfinderplus_V3.12_2024-05-02.2
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Select a virulence genes detection database: vfdb
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AMR genes detection database: amrfinderplus_V3.12_2024-05-02.2
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Virulence genes detection database: vfdb
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Select a StarmAMR database: staramr_downloaded_07042025_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502
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Select species for point mutation analysis using PointFinder: enterococcus_faecalis
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outputs:

‎workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection.ga‎

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"inputs": [
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{
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"description": "Select the database to identify AMR genes with AMRFinderPlus.",
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"name": "Select a AMR genes detection database"
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"name": "AMR genes detection database"
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}
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],
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"label": "Select a AMR genes detection database",
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"label": "AMR genes detection database",
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"name": "Input parameter",
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"outputs": [],
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"position": {
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"inputs": [
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{
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"description": "Select the database to identify virulence genes with ABRicate.",
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"name": "Select a virulence genes detection database"
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"name": "Virulence genes detection database"
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}
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],
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"label": "Select a virulence genes detection database",
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"label": "Virulence genes detection database",
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"name": "Input parameter",
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"outputs": [],
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"position": {

‎workflows/genome_annotation/functional-annotation/functional-annotation-protein-sequences/Functional_annotation_of_protein_sequences.ga‎

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]
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},
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"2": {
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"annotation": "EggNOG Mapper compares each protein sequence of the annotation to a huge set of ortholog groups from the EggNOG database.",
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"annotation": "EggNOG Mapper compares each protein sequence of the annotation to a huge set of ortholog groups from the eggNOG database.",
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"content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy4",
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"errors": null,
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"id": 2,

‎workflows/genome_annotation/functional-annotation/functional-annotation-protein-sequences/README.md‎

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This workflow uses eggNOG mapper and Interproscan for functional annotation of protein sequences.
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It can be used on proteins from any organism.
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EggNOG Mapper compares each protein sequence of the annotation to a huge set of ortholog groups from the EggNOG database. In this database, each ortholog group is associated with functional annotation like Gene Ontology (GO) terms or KEGG pathways. When the protein sequence of a new gene is found to be very similar to one of these ortholog groups, the corresponding functional annotation is transfered to this new gene.
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EggNOG Mapper compares each protein sequence of the annotation to a huge set of ortholog groups from the eggNOG database. In this database, each ortholog group is associated with functional annotation like Gene Ontology (GO) terms or KEGG pathways. When the protein sequence of a new gene is found to be very similar to one of these ortholog groups, the corresponding functional annotation is transfered to this new gene.
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InterProScan is a tool that analyses each protein sequence from our annotation to determine if they contain one or several of the signatures from InterPro. When a protein contains a known signature, the corresponding functional annotation will be assigned to it by InterProScan.
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‎workflows/microbiome/metagenomic-genes-catalogue/.dockstore.yml‎

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version: 1.2
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workflows:
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- name: main
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subclass: Galaxy
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publish: true
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primaryDescriptorPath: /metagenomic-genes-catalogue.ga
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testParameterFiles:
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- /metagenomic-genes-catalogue-tests.yml
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authors:
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- name: ABRomics
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email: [email protected]
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- name: abromics-consortium
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url: https://www.abromics.fr/
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- name: Hugo Lefeuvre
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orcid: 0009-0005-6834-4058

‎workflows/microbiome/metagenomic-genes-catalogue/CHANGELOG.md‎

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# Changelog
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## [1.0] - 2025-10-14
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- First release

‎workflows/microbiome/metagenomic-genes-catalogue/README.md‎

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# Genes catalogue generation from metagenomic reads
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This workflow generates genes catalogue from paired short reads.
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The workflow supports assembly using **MEGAHIT**.
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## Genes catalogue Annotation and Quality Control
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After assembly, CDS are detected from resulting contigs with **Prodigal** and the potential genes are clustered with **MMseqs2linclust**
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The following processing steps are then performed:
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- **Genes annotation** with Eggnog-mapper
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- **Taxonomic Assignment** using MMseqs2taxonomy
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- **Assembly Quality Control** via QUAST
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- **Abundance Estimation** per sample with CoverM
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- **AMR detection** with ABRicate, AMRFinderPlus and starAMR
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## Input Requirements
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Input reads must be quality-filtered, with host reads removed.
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- **Trimmed reads**: Quality-trimmed reads from individual samples, used solely for abundance estimation.

‎workflows/microbiome/metagenomic-genes-catalogue/metagenomic-genes-catalogue-tests.yml‎

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- doc: Test outline for Genes_catalogue_paired_collection_metaG_ABRomics
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job:
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Metagenomics Trimmed reads:
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class: Collection
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collection_type: list:paired
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elements:
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- class: Collection
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type: paired
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identifier: genes_catalogue_test
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elements:
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- class: File
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identifier: forward
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location: https://zenodo.org/records/17348100/files/genes_catalogue_R1.fastqsanger.gz
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- class: File
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identifier: reverse
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location: https://zenodo.org/records/17348100/files/genes_catalogue_R2.fastqsanger.gz
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eggNOG database: 5.0.2
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mmseqs2 taxonomy DB: UniRef50-17-b804f-07112025
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starAMR database: staramr_downloaded_07042025_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502
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Virulence genes detection database: vfdb
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AMR genes detection database: amrfinderplus_V3.12_2024-05-02.2
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outputs:
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MMseqs2 Taxonomy Filtered:
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asserts:
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has_text:
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text: "domain"
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has_n_columns:
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n: 4
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Eggnog Annotation Filtered:
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asserts:
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has_text:
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text: "Contig id"
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has_n_columns:
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n: 21
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MMseqs2 Taxonomy Kraken:
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asserts:
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has_text:
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text: "cellular root"
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has_n_columns:
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n: 6
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Argnorm AMRfinderplus Report:
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asserts:
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has_text:
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text: "Protein identifier"
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Eggnog Annotations:
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asserts:
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has_text:
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text: "#query"
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has_n_columns:
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n: 21
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Resfinder:
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asserts:
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has_text:
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text: "Isolate ID"
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has_n_columns:
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n: 13
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Abricate Virulence Report:
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asserts:
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has_text:
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text: "#FILE"
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has_n_columns:
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n: 15
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Amrfinderplus Report:
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asserts:
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has_text:
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text: "Protein identifier"
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has_n_columns:
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n: 22
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Tooldistillator Summarize Collection:
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element_tests:
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genes_catalogue_test:
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asserts:
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- that: has_text
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text: "megahit_report"
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- that: has_text
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text: "quast_report"
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- that: has_text
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text: "prodigal_report"
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- that: has_text
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text: "coverm_report"
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Tooldistillator Summarize Catalogue:
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asserts:
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- that: has_text
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text: "eggnogmapper_report"
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- that: has_text
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text: "mmseqs2linclust_report"
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- that: has_text
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text: "staramr_report"
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- that: has_text
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text: "mmseqs2taxonomy_report"
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- that: has_text
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text: "abricate_report"
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- that: has_text
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text: "amrfinderplus_report"
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- that: has_text
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text: "argnorm_report"

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