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Add FAIRyMAGs Taxonomic Binning Evaluation Workflow #923
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4c3250a
Add FAIRyMAGs Taxonomic Binning Evaluation Workflow
SantaMcCloud 7f9e3a1
fix linting
SantaMcCloud 1afafbd
linting
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fix linting now
SantaMcCloud b304f5a
fix some test
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change file
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review changes
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labels
SantaMcCloud e21be0b
update zanodo data
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wrong url
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typo
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review changes and remove subworkflow
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update WF and test
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add release tag
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add the correct DB version for iwc
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Restart test
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update test
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Merge branch 'add_tax_binning_eva' of https://github.com/SantaMcCloud…
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Change input data
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change input to shorter version
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11 changes: 11 additions & 0 deletions
11
workflows/microbiome/taxonomic-binning-evaluation/.dockstore.yml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| version: 1.2 | ||
| workflows: | ||
| - name: main | ||
| subclass: Galaxy | ||
| publish: true | ||
| primaryDescriptorPath: /FAIRyMAGs-taxonomic-binning-evaluation.ga | ||
| testParameterFiles: | ||
| - /FAIRyMAGs-taxonomic-binning-evaluation-tests.yml | ||
| authors: | ||
| - name: Santino Faack | ||
| orcid: 0009-0004-0382-2023 |
5 changes: 5 additions & 0 deletions
5
workflows/microbiome/taxonomic-binning-evaluation/CHANGELOG.md
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| # Changelog | ||
|
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||
| ## [1.0] - 2025-07-31 | ||
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| - First release |
53 changes: 53 additions & 0 deletions
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.../microbiome/taxonomic-binning-evaluation/FAIRyMAGs-taxonomic-binning-evaluation-tests.yml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| - doc: Test outline for FAIRyMAGs-taxonomic-binning-evaluation | ||
| job: | ||
| Biobox File: | ||
| class: Collection | ||
| collection_type: list | ||
| elements: | ||
| - class: File | ||
| identifier: marine_pooled_gsb_trimmed | ||
| location: https://zenodo.org/records/16740696/files/Biobox_File(s)_marine_pooled_gsb_trimmed.tabular | ||
| Assemblies: | ||
| class: Collection | ||
| collection_type: list | ||
| elements: | ||
| - class: File | ||
| identifier: marine_pooled_gsa_trimmed | ||
| location: https://zenodo.org/records/16740696/files/Assemblyies_marine_pooled_gsa_trimmed.fasta | ||
| Reads: | ||
| class: Collection | ||
| collection_type: list:paired | ||
| elements: | ||
| - class: Collection | ||
| type: paired | ||
| identifier: _trimmed | ||
| elements: | ||
| - class: File | ||
| identifier: forward | ||
| location: https://zenodo.org/records/16740696/files/Reads_forward.fastqsanger | ||
| - class: File | ||
| identifier: reverse | ||
| location: https://zenodo.org/records/16740696/files/Reads_reverse.fastqsanger | ||
| outputs: | ||
| AMBER HTML Report: | ||
| asserts: | ||
| - that: has_text | ||
| text: AMBER Assessment of Metagenome BinnERs | ||
| AMBER Result Table: | ||
| asserts: | ||
| - has_n_columns: | ||
| n: 41 | ||
| - has_n_lines: | ||
| n: 58 | ||
| AMBER Genome Metric: | ||
| asserts: | ||
| - has_n_columns: | ||
| n: 16 | ||
| - has_n_lines: | ||
| n: 6691 | ||
| AMBER Bin Metric: | ||
| asserts: | ||
| - has_n_columns: | ||
| n: 20 | ||
| - has_n_lines: | ||
| n: 9805 | ||
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This file is 3GB, that is far too large. I would suggest making this a megabyte or less.
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this was the first test data which did run. I will minimize it but it will take time since only 1 tool need specific reads it seems to work. I will pick some and try it with it to see if it works better and faster
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@mvdbeek i did change the file size now and i hope the current size is fine for it!
The i did test the WFs locally on the .EU serve via planemo and all test where fine i hope that there will no problem in github this time and if so could you help me to reolve them? Thank you in advance for this!!