mags-taxonomy-annotation/main v0.1
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Tests This workflow performs taxonomic classification of an input sequence collection (e.g., bins from SemiBin2 or MetaBat) using GTDB-Tk and maps the resulting taxonomy to NCBI taxIDs and names to reconcile differences between classification systems.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| GTDB-tk Database | GTDB-tk Database | GTDB-tk Database used for Bin Taxonomy Classification |
|
| Sequence collection | Sequence collection | Provide a collection of MAGs from dREP or another binning tool. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | GTDB-Tk Classify genomes | toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.5.2+galaxy1 |
| 3 | Concatenate multiple datasets or collections | cat1 |
| 4 | Cut | Cut1 |
| 5 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 6 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 7 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 8 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 |
| 9 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 |
| 10 | Remove beginning | Remove beginning1 |
| 11 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 12 | NCBI-GTDB map | toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 |
| 13 | Cut | Cut1 |
| 14 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 |
| 15 | Name2taxid | toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 |
| 16 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 17 | Paste | Paste1 |
| 18 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 |
| 19 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 |
| 20 | Cut | Cut1 |
| 21 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 |
| 22 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 23 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.33+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| GTDB-Tk summary files | GTDB-Tk summary files | n/a |
|
| GTDB-NCBI mapping | GTDB-NCBI mapping | n/a |
|
| NCBI names to taxIDs mapping | NCBI names to taxIDs mapping | n/a |
|
| full GTDB to NCBI mapping | full GTDB to NCBI mapping | n/a |
|
| MultiQC HTML report | MultiQC HTML report | n/a |
|
Version History
v0.1 (earliest) Created 4th Mar 2026 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.14f041a8
Creators and Submitter
Views: 345 Downloads: 1682 Runs: 0
Created: 4th Mar 2026 at 03:01
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