Convert duplicate-keyed asserts blocks to list form (passing subset)#1275
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mvdbeek merged 1 commit intoJul 13, 2026
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jmchilton
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wm75
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July 10, 2026 18:22
YAML silently collapses duplicate mapping keys, so `asserts:` blocks with repeated `has_text:` / `has_line:` / `has_text_matching:` entries were only running the *last* assertion per type — the rest were dead. Convert to list form (`- that: has_text` ...) so each assertion is a distinct item and actually runs. Semantic change: tests that silently passed earlier assertions may now fail if the previously-dropped assertion text doesn't actually match tool output. Surfaced by the Galaxy gxwf workflow-test validator IWC sweep.
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Attention: deployment failure! https://github.com/galaxyproject/iwc/actions/runs/29231569359 |
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Summary
YAML silently collapses duplicate mapping keys, so
asserts:blocks that repeat an assertion type (has_text:,has_line:,has_text_matching:) only ran the last assertion per type — every earlier assertion was silently dropped by the loader and never executed. This converts the affected workflow-tests files to list form so every assertion runs:Successor to closed #1217, reduced to the files whose tests are genuinely green with this change. Files whose tests fail/error are split into their own PRs.
Files (6)
bacterial_quality_and_contamination_control_post_assembly-tests.ymlquality_and_contamination_control_raw_reads-tests.ymlhost-or-contamination-removal-on-long-reads-tests.ymlshort-read-quality-control-and-trimming-tests.ymlpe-artic-variation-tests.ymlgenotype-variant-calling-wgs-pe-test.ymlSplit out
bcftools concatSIGSEGV (unrelated to the assertion conversion). IWC only tests changed workflows, so touching that file merely surfaced the crash.How this was found
Galaxy's new
gxwf validate-testsvalidator swept IWC workflow-tests against the PydanticTestsmodel;ordered_loadraises on duplicate mapping keys (per YAML 1.2), surfacing these authoring bugs.FOR CONTRIBUTOR: