metagenomic-genes-catalogue/main
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Tests Metagenomic analysis, from raw reads to gene catalog. Uses Megahit to assemble contigs and Prodgial to predict CDSs on contigs to provide the gene catalog. Finally, functional, taxonomic, and antimicrobial resistance information is provided.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| AMR genes detection database | AMR genes detection database | Select the database to identify AMR genes with AMRFinderPlus. |
|
| Full genes catalogue | Full genes catalogue | Set it to Yes if you want to have the full gene catalogue. Functionnal and taxonomical annotation are made on full clustered CDS |
|
| Metagenomics Trimmed reads | Metagenomics Trimmed reads | Input for this workflow is a paired collection from metagenomics trimmed reads |
|
| Virulence genes detection database | Virulence genes detection database | Select the database to identify virulence genes with ABRicate. |
|
| eggNOG database | eggNOG database | Select the database to identify genes function with eggnogmapper |
|
| mmseqs2 taxonomy DB | mmseqs2 taxonomy DB | Select the database to identify taxonomy with mmseqs2 |
|
| starAMR database | starAMR database | Select the database to identify AMR elements with starAMR. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | MEGAHIT | toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy2 |
| 8 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 9 | FASTA-to-Tabular | Convert to tabular format to make it easier to modify the contig ID. toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
| 10 | Quast | toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.3.0+galaxy1 |
| 11 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 12 | Add input name as column | Adds the sample name to the column corresponding to the initial ID. Allows you to create a unique ID for each sample. toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.2.0 |
| 13 | Tabular-to-FASTA | Return to the fasta format with unique IDs. toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
| 14 | Concatenate datasets | Concatenate contigs from each sample toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.5+galaxy2 |
| 15 | Prodigal Gene Predictor | toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0 |
| 16 | MMseqs2 full catalogue Sequence Clustering | toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_easy_linclust_clustering/mmseqs2_easy_linclust_clustering/17-b804f+galaxy0 |
| 17 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 18 | AMRFinderPlus | toolshed.g2.bx.psu.edu/repos/iuc/amrfinderplus/amrfinderplus/3.12.8+galaxy0 |
| 19 | ABRicate | toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/1.0.1 |
| 20 | staramr | toolshed.g2.bx.psu.edu/repos/iuc/staramr/staramr_search/0.11.0+galaxy3 |
| 21 | argNorm | toolshed.g2.bx.psu.edu/repos/iuc/argnorm/argnorm/1.0.0+galaxy0 |
| 22 | table rename column | toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy1 |
| 23 | Remove columns | toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
| 24 | Genes catalogue AMR specific part | Workflow for retrieving the IDs of contigs and CDSs of antibiotic resistance genes and filtering Prodigal output to retrieve a catalogue of antibiotic resistance genes and potential genes present on the same contig as the ARG. |
| 25 | Remove beginning | Remove beginning1 |
| 26 | Remove columns | toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
| 27 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 28 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 29 | Remove columns | toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
| 30 | MMseqs2 ARGs Sequence Clustering | toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_easy_linclust_clustering/mmseqs2_easy_linclust_clustering/17-b804f+galaxy0 |
| 31 | SeqKit translate | toolshed.g2.bx.psu.edu/repos/iuc/seqkit_translate/seqkit_translate/2.12.0+galaxy0 |
| 32 | eggNOG Mapper | toolshed.g2.bx.psu.edu/repos/galaxyp/eggnog_mapper/eggnog_mapper/2.1.8+galaxy4 |
| 33 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 34 | MMseqs2 Taxonomy Assignments | toolshed.g2.bx.psu.edu/repos/iuc/mmseqs2_taxonomy_assignment/mmseqs2_taxonomy_assignment/17-b804f+galaxy0 |
| 35 | table rename column | toolshed.g2.bx.psu.edu/repos/recetox/table_pandas_rename_column/table_pandas_rename_column/2.2.3+galaxy1 |
| 36 | CoverM contig | toolshed.g2.bx.psu.edu/repos/iuc/coverm_contig/coverm_contig/0.7.0+galaxy0 |
| 37 | Krakentools: Convert kraken report file | toolshed.g2.bx.psu.edu/repos/iuc/krakentools_kreport2krona/krakentools_kreport2krona/1.2.1+galaxy0 |
| 38 | Column join | toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3 |
| 39 | Krona pie chart | toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
| 40 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Megahit Contigs Output | Megahit Contigs Output | n/a |
|
| Report Tabular Meta | Report Tabular Meta | n/a |
|
| Report HTML Meta | Report HTML Meta | n/a |
|
| Concatenate Datasets | Concatenate Datasets | n/a |
|
| Prodigal Genes Sequences | Prodigal Genes Sequences | n/a |
|
| Prodigal Genes Translation | Prodigal Genes Translation | n/a |
|
| AMRFinderplus Report | AMRFinderplus Report | n/a |
|
| Abricate Virulence Report | Abricate Virulence Report | n/a |
|
| Detailed Summary | Detailed Summary | n/a |
|
| Plasmidfinder | Plasmidfinder | n/a |
|
| Resfinder | Resfinder | n/a |
|
| Argnorm AMRfinderplus Report | Argnorm AMRfinderplus Report | n/a |
|
| Seqkit Protein Translation | Seqkit Protein Translation | n/a |
|
| Eggnog Report Orthologs | Eggnog Report Orthologs | n/a |
|
| Eggnog Seed Orthologs | Eggnog Seed Orthologs | n/a |
|
| Eggnog Annotations | Eggnog Annotations | n/a |
|
| MMseqs2 representative sequences | MMseqs2 representative sequences | n/a |
|
| MMseqs2 Taxonomy Tabular | MMseqs2 Taxonomy Tabular | n/a |
|
| MMseqs2 Taxonomy Kraken | MMseqs2 Taxonomy Kraken | n/a |
|
| CoverM contig | CoverM contig | n/a |
|
| MMseqs2 Taxonomy Krona | MMseqs2 Taxonomy Krona | n/a |
|
| MultiQC Report | MultiQC Report | n/a |
|
Version History
v1.2.1 (latest) Created 25th Feb 2026 at 03:01 by WorkflowHub Bot
Updated to v1.2.1
Frozen
v1.2.1c5bb240
v1.0 (earliest) Created 30th Nov 2025 at 03:02 by WorkflowHub Bot
Updated to v1.0
Frozen
v1.0
fde7261
Creators and SubmitterActivity
Views: 1211 Downloads: 8794 Runs: 8
Created: 30th Nov 2025 at 03:01
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