Finalize the CAMI Binning Benchmark Workflow

[paulzierep]

• Update Tools
• Update DBs
• Add MaxBin2
• Clean GTDB2NCBI-TaxID Sub-workflow (IWC). Output should be a table (bin2taxid-map) containing Bin ID, GTDB name, NCBI-Name, NCBI-TaxID. This should include Archaea and Bacteria. In fact, the output of GTDB summary should be extended with these columns. This is also useful for the main workflow.
• Clean Biobox-Add-TaxID tool. A simple tool using the created table. That updates the biobox with another column. The tool should be able to work with bin2taxid-map, but also with contig2taxid (which could be generated with kraken2).
• Taxonomic binning should be optional.

Optional:

• CAT2NCBI-TaxID workflow, generating an identical output as GTDB2NCBI-TaxID Sub-workflow (bin2taxid-map). Compliant with the Biobox-Add-TaxID tool.

[SantaMcCloud]

Clean GTDB2NCBI-TaxID Sub-workflow (IWC). Output should be a table (bin2taxid-map) containing Bin ID, GTDB name, NCBI-Name, NCBI-TaxID. This should include Archaea and Bacteria. In fact, the output of GTDB summary should be extended with these columns. This is also useful for the main workflow.

I can rework my script for this which can modify the inputed GTDB summary file(s) and to be able to give the bin2taxid-map file. Just to be clear the modifieng and the creating of a bin2taxid-map file should work together with the modifing the biobox file or should the scrip either do one thing at the time?

Clean Biobox-Add-TaxID tool. A simple tool using the created table. That updates the biobox with another column. The tool should be able to work with bin2taxid-map, but also with contig2taxid (which could be generated with kraken2).

I also can change my scrip to work with like this or should there be a new scrip/tool make this possible?

[paulzierep]

Clean GTDB2NCBI-TaxID Sub-workflow (IWC). Output should be a table (bin2taxid-map) containing Bin ID, GTDB name, NCBI-Name, NCBI-TaxID. This should include Archaea and Bacteria. In fact, the output of GTDB summary should be extended with these columns. This is also useful for the main workflow.

I can rework my script for this which can modify the inputed GTDB summary file(s) and to be able to give the bin2taxid-map file. Just to be clear the modifieng and the creating of a bin2taxid-map file should work together with the modifing the biobox file or should the scrip either do one thing at the time?

I would prefer to have one workflow that generates the bin2taxid-map file, I think the tools you added NCBI-GTDB map and Name2taxid are enough. You just need to collapse the Archaea and Bacteria files of the collection (https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fcollapse_collections%2Fcollapse_dataset%2F5.1.0&version=latest) output of GTDB, then combine the outputs of NCBI-GTDB map and Name2taxid with the summary file. https://usegalaxy.eu/?tool_id=Paste1&version=latest should work for this.

Modifying the biobox file should be an additional step with one tool as described below.

Clean Biobox-Add-TaxID tool. A simple tool using the created table. That updates the biobox with another column. The tool should be able to work with bin2taxid-map, but also with contig2taxid (which could be generated with kraken2).

I also can change my scrip to work with like this or should there be a new scrip/tool make this possible?

You can change your script to only use the bin2taxid-map and biobox as input. But then I would prefer, that the updated tool, excludes the previous options, its was too custom and complicated. But it can also be an additional tool up to you.

[SantaMcCloud]

I would prefer to have one workflow that generates the bin2taxid-map file, I think the tools you added NCBI-GTDB map and Name2taxid are enough. You just need to collapse the Archaea and Bacteria files of the collection (https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fnml%2Fcollapse_collections%2Fcollapse_dataset%2F5.1.0&version=latest) output of GTDB, then combine the outputs of NCBI-GTDB map and Name2taxid with the summary file. https://usegalaxy.eu/?tool_id=Paste1&version=latest should work for this.

Modifying the biobox file should be an additional step with one tool as described below.

Here is a sub-workflow which generated a binid2taxid file and modify the GTDB-Tk file:
Workflow: https://usegalaxy.eu/u/santinof/w/gtdb2ncbi-taxid-sub-workflow
Example history: https://usegalaxy.eu/u/santinof/h/gtdb2ncbi-taxid-sub-workflow-example

You can change your script to only use the bin2taxid-map and biobox as input. But then I would prefer, that the updated tool, excludes the previous options, its was too custom and complicated. But it can also be an additional tool up to you.

I did change my script to work with either kraken2 output or the output from the sub-workflow above.
https://github.com/SantaMcCloud/biobox_add_taxid

[SantaMcCloud]

Update Tools

Current list of all tools used in the Workflow with their version:

Name	Current Galaxy Version	Available Version	Wrapper updated	Notes
Bowtie2	2.5.3	2.5.4		has an open PR but it seems that they have to adjust Galaxy a bit to make this update
Fairy	0.5.7	0.5.7	-
CAMI AMBER	2.0.7	2.0.7	-
CONCOCT	1.1.0	1.1.0	-
MaxBin2	2.2.7	?	?	The page is missing which is linked in IUC
DAS Tool	1.1.7	1.17	-
MetaBAT2	2.15 (updated to 2.17)	2.17	✅	is merged
SemiBin	2.0.2	2.1.0		has an open PR and somebody is working on it. The last commit was pushed around 2 weeks and it still fails. Depend on how fast this should be done i can finish this PR
GTDB-Tk	2.4.0	2.4.0	-
NCBI-GTDB map	0.1.9	0.1.9	-
Name2Taxid	0.18.0	0.18.0	-
Biobox_add_taxid	0.6	1.0.0		My Tool will be changed when approved by Paul

Update DBs

Current list of all DBs used in the Workflow with their version plus the DB from Kraken2:

Name	Current Galaxy Version	Available Version	DM updated if needed	Notes
Kraken2	2024-09-04	2024-12-28	✅	The newest version was merged. Any admin can downlaod the newest Dbs when galaxy is updated
NCBI	2024-06-05	2025-01-25	-	The DM always pulls the newest version -> any admin can do this update anytime
SemiBin2	?	?	?	I think it is the latest version but it is hard to tell since i can not access the table and there is no date written in the name
GTDB-Tk	220	220	-
NCBI-GTDB map	220	220	-