mags-taxonomy-annotation/main
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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 kMetaShot (optional). GTDB-Tk taxonomy is mapped to NCBI taxIDs and names to reconcile differences between NCBI/GTDB taxonomies.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| GTDB-Tk Database | GTDB-Tk Database | GTDB-Tk Database used for Bin Taxonomy Classification |
|
| MAGs taxonomic classification with kMetaShot (optional) | MAGs taxonomic classification with kMetaShot (optional) | Option to add MAGs taxonomic classification with kMetaShot |
|
| Sequence collection | Sequence collection | Provide a collection of MAGs from dRep or another binning tool. |
|
| ass2ref for kMS | ass2ref for kMS | ass2ref is the level of reliability to set for strain taxonomic classification [0, 1]. |
|
| kMetaShot Database | kMetaShot Database | kMetaShot Database used for MAGs Taxonomy Classification |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | GTDB-Tk Classify genomes | toolshed.g2.bx.psu.edu/repos/iuc/gtdbtk_classify_wf/gtdbtk_classify_wf/2.5.2+galaxy1 |
| 6 | kMetaShot taxonomic classification of MAGs | This is the step for the optional execution of kMetaShot. It is an alignment-free algorithm for prokaryotes classification. toolshed.g2.bx.psu.edu/repos/bgruening/kmetashot/kmetashot/2.0+galaxy2 |
| 7 | Concatenate multiple datasets or collections | cat1 |
| 8 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 9 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 10 | Cut | Cut1 |
| 11 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
| 12 | Convert | Convert characters1 |
| 13 | Convert | Convert characters1 |
| 14 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 15 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 16 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 |
| 17 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 |
| 18 | Remove beginning | Remove beginning1 |
| 19 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 20 | NCBI-GTDB map | toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 |
| 21 | Cut | Cut1 |
| 22 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 |
| 23 | Name2taxid | toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 |
| 24 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 25 | Paste | Paste1 |
| 26 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy3 |
| 27 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 |
| 28 | Cut | Cut1 |
| 29 | Join | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.5+galaxy3 |
| 30 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 31 | 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
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Views: 656 Downloads: 4141 Runs: 0
Created: 4th Mar 2026 at 03:01
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