Update/arborator gas 0.1.3 #27
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apetkau
commented
Jan 15, 2025
| // The goal of this test is to make sure that the produced tree has correct branches | ||
| // So other comparisons for metadata, etc, were removed | ||
| def actual_arborator_tree_1 = path("$launchDir/results/arborator/1_tree.nwk") | ||
| def expected_arborator_tree_1 = path("$baseDir/tests/data/arborator/1/tree_all_single_partition.nwk") |
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I included this test which focuses on verifying the produced newick file when all genomes are in the same partition is valid (e.g., has correct branch lengths after updating GAS to 0.1.3). I removed all other checks (e.g., related to metadata/summaries) from this test case.
For additional information, see the screenshot below. The left tree is the expected_arborator_tree_1, with correct branch lengths (all leaves line up on the right side). The right tree is the older, incorrect tree when using the older arborator container with an older version of the GAS dependency (you can see leaves do not all line up on the right side).
For more context on this issue, see phac-nml/genomic_address_service#15
emarinier
approved these changes
Jan 15, 2025
CHANGELOG.md
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| @@ -3,6 +3,10 @@ | |||
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) | |||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | |||
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| ## [0.3.2] - 2025-01-15 | |||
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| - Updated the build of the arborator container in order to update the `genomic_address_service` dependency to [version 0.1.3](https://github.com/phac-nml/genomic_address_service/releases/tag/0.1.3), which fixes an issue with branch lengths in newick files. | |||
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Newick should be capitalized.
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Good catch. Thanks. Fixed 257826e
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| tag "pipeline" | ||
| tag "pipeline_all" |
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Is the double tag here intentional?
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Yes. I wanted to have a separate tag so I could run this test alone.
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Updates the container for arborator in order to update the
genomic_address_servicedependency to version 0.1.3 to fix an issue with branch lengths in newick files.PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.