Collect information of pipeline with different assembly / binning strategies

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/24

Create a nice overview mindmap of assembly, binning methods

Update IWC workflow to include the grouping

https://github.com/galaxyproject/iwc/pull/975

see: https://usegalaxy.eu/workflows/run?id=40d2c7ac42bd5302 for how to use the readme and help section of workflows. The readme in https://github.com/galaxyproject/iwc/tree/main/workflows/virology/generic-non-segmented-viral-variant-calling is like a combination of the two.

Add annotations to IWC workflow (on workflow canvas)

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/73

Test "frugal" spades - a new mode of spades that consumes less memory but doesn't produce the scaffolds file

Multi text input for tools in the workflow

https://github.com/galaxyproject/galaxy/issues/21015

Stefan Kranz, Paul

https://usegalaxy.eu/u/skranz/w/imported-metagenome-assembled-genomes-mags-generation---only-ont-version

Low resource workflow for high troughput (less mags though)

We could make a low resource version, that uses single assembly, fairy and only one of the binners (the best from the benchmark), this would allow us to screen large sample sets with the downside of fewer mags.

Add tool to compare MAGs to MGnify MAGs catalogue

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/76

Find a way to map assembly and reads all-vs-all (requirement for co-abundance)

Update CONCOCT wrapper to support co-abundance

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/59

Update maxbin2 wrapper to support co-abundance

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/59

https://github.com/galaxyproject/tools-iuc/pull/7285

The tool itself is in Galaxy but the utiltiy script which was a part of the tool is needed since Bowtie2 BAM files are not working with COMEBin

https://github.com/galaxyproject/tools-iuc/pull/7285

https://github.com/galaxyproject/tools-iuc/pull/7347

PR is created the problem was that SemiBin did swap the file format of saving the ML model. Also a second PR had do be done to add the new file format to galaxy.

Add fallback for binners when they do not fin bins

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/65

Update CheckM2 and CheckM2 DM to the current version

https://github.com/galaxyproject/tools-iuc/pull/6861

https://github.com/galaxyproject/tools-iuc/pull/7338

Collect tools, workflows that should be added

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/60

https://github.com/galaxyproject/tools-iuc/pull/7263

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/58

https://github.com/galaxyproject/tools-iuc/pull/6807

[nf-core/seqsubmit] Work on the MAGs submission using MGnify ENA submission tools

Create notebook of your favorite MAGs figure

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/54

Everybody is free to add any kind of visualizaiton as a PR to https://github.com/usegalaxy-eu/FAIRyMAGs/tree/main/Analysis_Scripts/MAGs-visualizations/Hackathon-Notebooks-2025, add your name to the notebook, we can inspect the plots at the end of the week and create a tool based on that !

Create package with the figure to import it to galaxy as tool

https://github.com/SantaMcCloud/MAGs-visualization

I did all and modified some plots which Paul and i did create with the notebook given in the FAIRyMAG GitHub

Test IWC workflows on usegalaxy.org.au

1) Metagenome-Assembled Genomes (MAGs) generation
https://iwc.galaxyproject.org/workflow/mags-building-main/

Step 29: SemiBin
- Using version '2.1.0+galaxy0' instead of version '2.0.2+galaxy1' specified in this workflow.
Step 34: MaxBin2
- No value found for 'Input type'. Using default: 'rds'.
- No value found for 'Reads file(s)'. Using default: ''.
- No value found for 'Output abundances'. Using default: 'False'.
- No value found for 'Reassembly'. Using default: 'False'.
- No value found for 'Advanced options'. Using default: 'no'.
- Using version '2.2.7+galaxy2' instead of version '2.2.7+galaxy6' specified in this workflow.
Step 42: Binette
- Using version '1.1.2+galaxy0' instead of version '1.1.1+galaxy0' specified in this workflow.

2) Metagenome-Assembled Genomes (MAGs) generation - only ONT version
https://usegalaxy.eu/u/paulzierep/w/metagenome-assembled-genomes-mags-generation---only-ont-version


Step 21: SemiBin
- Using version '2.1.0+galaxy0' instead of version '2.0.2+galaxy1' specified in this workflow.
Step 26: MaxBin2
- No value found for 'Input type'. Using default: 'rds'.
- No value found for 'Reads file(s)'. Using default: ''.
- No value found for 'Output abundances'. Using default: 'False'.
- No value found for 'Reassembly'. Using default: 'False'.
- No value found for 'Advanced options'. Using default: 'no'.
- Using version '2.2.7+galaxy2' instead of version '2.2.7+galaxy6' specified in this workflow.
Step 34: Binette
- Using version '1.1.2+galaxy0' instead of version '1.1.1+galaxy0' specified in this workflow.

3) Group Assignment for Co-Assembly
https://usegalaxy.eu/u/mina24/w/preprocessing-for-group-assignment-co-assembly-7
- Step 8: Concatenate
- Using version '1.0' instead of version '1.4.3' specified in this workflow.

4) Metagenome-Assembled Genomes (MAGs) generation
https://usegalaxy.eu/u/paulzierep/w/mags-generation
Step 29: SemiBin
- Using version '2.1.0+galaxy0' instead of version '2.0.2+galaxy1' specified in this workflow.
Step 34: MaxBin2
- No value found for 'Input type'. Using default: 'rds'.
- No value found for 'Reads file(s)'. Using default: ''.
- No value found for 'Output abundances'. Using default: 'False'.
- No value found for 'Reassembly'. Using default: 'False'.
- No value found for 'Advanced options'. Using default: 'no'.
- Using version '2.2.7+galaxy2' instead of version '2.2.7+galaxy6' specified in this workflow.
Step 42: Binette
- Using version '1.1.2+galaxy0' instead of version '1.0.5+galaxy1' specified in this workflow.
Step 44: checkm2
- Using version '1.0.2+galaxy1' instead of version '1.0.2+galaxy0' specified in this workflow.
Step 48: checkm2
- Using version '1.0.2+galaxy1' instead of version '1.0.2+galaxy0' specified in this workflow.


5) CAMI Binning Benchmark Workflow
https://usegalaxy.eu/u/santinof/w/fairymags-binning-evaluation-v11
Step 33: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_add/cami_amber_add/2.0.7+galaxy0
- Tool is not installed
Step 40: SemiBin
- Using version '2.1.0+galaxy0' instead of version '2.0.2+galaxy0' specified in this workflow.
Step 44: MaxBin2
- No value found for 'Input type'. Using default: 'rds'.
- No value found for 'Reads file(s)'. Using default: ''.
- No value found for 'Output abundances'. Using default: 'False'.
- No value found for 'Reassembly'. Using default: 'False'.
- No value found for 'Advanced options'. Using default: 'no'.
- Using version '2.2.7+galaxy2' instead of version '2.2.7+galaxy6' specified in this workflow.
Step 46: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.6+galaxy0
- Tool is not installed
Step 50: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.6+galaxy0
- Tool is not installed
Step 52: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.6+galaxy0
- Tool is not installed
Step 57: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.6+galaxy0
- Tool is not installed
Step 62: toolshed.g2.bx.psu.edu/repos/iuc/das_tool/das_tool/1.1.7+galaxy1
- Tool is not installed
Step 65: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 66: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 67: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 68: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 69: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.6+galaxy0
- Tool is not installed
Step 70: Binette
- Using version '1.1.2+galaxy0' instead of version '1.0.5+galaxy1' specified in this workflow.
Step 71: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 73: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.6+galaxy0
- Tool is not installed
Step 74: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 76: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 77: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber/cami_amber/2.0.7+galaxy0
- Tool is not installed

6) CAMI Binning Benchmark Workflow
https://usegalaxy.eu/u/santinof/w/fairymags-tax-binning-evaluation

Step 33: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_add/cami_amber_add/2.0.7+galaxy0
- Tool is not installed
Step 40: SemiBin
- Using version '2.1.0+galaxy0' instead of version '2.0.2+galaxy2' specified in this workflow.
Step 55: FAIRyMAGs GTDB-Tk subworkflow
- [ "toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0 is not installed", [ "toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 is not installed", "toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 is not installed" ], "toolshed.g2.bx.psu.edu/repos/iuc/biobox_add_taxid/biobox_add_taxid/1.2+galaxy0 is not installed" ]
- { "gtdbtk_db": "Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'." }
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 56: FAIRyMAGs GTDB-Tk subworkflow
- [ "toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0 is not installed", [ "toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 is not installed", "toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 is not installed" ], "toolshed.g2.bx.psu.edu/repos/iuc/biobox_add_taxid/biobox_add_taxid/1.2+galaxy0 is not installed" ]
- { "gtdbtk_db": "Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'." }
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 57: FAIRyMAGs GTDB-Tk subworkflow
- [ "toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0 is not installed", [ "toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 is not installed", "toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 is not installed" ], "toolshed.g2.bx.psu.edu/repos/iuc/biobox_add_taxid/biobox_add_taxid/1.2+galaxy0 is not installed" ]
- { "gtdbtk_db": "Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'." }
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 58: FAIRyMAGs GTDB-Tk subworkflow
- [ "toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0 is not installed", [ "toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 is not installed", "toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 is not installed" ], "toolshed.g2.bx.psu.edu/repos/iuc/biobox_add_taxid/biobox_add_taxid/1.2+galaxy0 is not installed" ]
- { "gtdbtk_db": "Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'." }
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 59: toolshed.g2.bx.psu.edu/repos/iuc/das_tool/das_tool/1.1.7+galaxy1
- Tool is not installed
Step 61: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 62: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 63: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 64: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 65: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 66: FAIRyMAGs GTDB-Tk subworkflow
- [ "toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0 is not installed", [ "toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 is not installed", "toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 is not installed" ], "toolshed.g2.bx.psu.edu/repos/iuc/biobox_add_taxid/biobox_add_taxid/1.2+galaxy0 is not installed" ]
- { "gtdbtk_db": "Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'." }
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 68: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 69: FAIRyMAGs GTDB-Tk subworkflow
- [ "toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0 is not installed", [ "toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 is not installed", "toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 is not installed" ], "toolshed.g2.bx.psu.edu/repos/iuc/biobox_add_taxid/biobox_add_taxid/1.2+galaxy0 is not installed" ]
- { "gtdbtk_db": "Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'." }
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 70: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 71: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber/cami_amber/2.0.7+galaxy0
- Tool is not installed

7) GTDB2NCBI-TaxID subworkflow
https://usegalaxy.eu/u/santinof/w/fairymags-gtdb-tk-subworkflow-v1

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/cami_amber_convert/cami_amber_convert/2.0.7+galaxy0
- Tool is not installed
Step 5: GTDB-Tk Classify genomes
- Parameter 'gtdbtk_db': an invalid option ('full_database_release_220_downloaded_2024-10-28') was selected (valid options: full_database_release_220_downloaded_2024-10-19) Using default: 'full_database_release_220_downloaded_2024-10-19'.
Step 6: GTDB2NCBI-TaxID Subworkflow
- [ "toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0 is not installed", "toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0 is not installed" ]
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 7: toolshed.g2.bx.psu.edu/repos/iuc/biobox_add_taxid/biobox_add_taxid/1.2+galaxy0
- Tool is not installed

8) FARIyMAGs GTDB-Tk subworkflow
https://usegalaxy.eu/u/santinof/w/gtdb2ncbi-taxid-subworkflow

Step 2: Concatenate multiple datasets
- Using version '1.0' instead of version '1.4.3' specified in this workflow.
Step 8: toolshed.g2.bx.psu.edu/repos/iuc/gtdb_to_taxdump/gtdb_to_taxdump/0.1.9+galaxy0
- Tool is not installed
Step 11: toolshed.g2.bx.psu.edu/repos/iuc/name2taxid/name2taxid/0.20.0+galaxy0
- Tool is not installed

Detail: testing https://iwc.galaxyproject.org/workflow/mags-building-main/

https://github.com/usegalaxy-eu/FAIRyMAGs/issues/74. Some tools were missing, now installed (see above, by Saim)

Andrew Mike Anna AU

Testing: https://usegalaxy.eu/u/paulzierep/w/preprocessing-for-mags

Testing: https://usegalaxy.eu/u/mina24/w/preprocessing-for-group-assignment-co-assembly-7

Testing: https://usegalaxy.eu/u/paulzierep/w/host-contamination-removal

Testing: https://usegalaxy.eu/u/santinof/w/fairymags-binning-evaluation-v11

Some steps fail Testing History: https://usegalaxy.org.au/u/saim_12/h/fairymags-cami-binning-benchmark-workflow

Testing: https://usegalaxy.eu/u/santinof/w/gtdb2ncbi-taxid-subworkflow

Testing the updated MAGs generation workflow

as for line 48, but using most recent update for workflow in https://github.com/galaxyproject/iwc/pull/975