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Species reconfigured
- #194
#194
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SimoneScrima
merged 16 commits into
dev
ssi-dk/MMASeq:dev
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species_reconfigured
ssi-dk/MMASeq:species_reconfigured
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Aug 6, 2026
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Species reconfigured
#194
SimoneScrima
merged 16 commits into
dev
ssi-dk/MMASeq:dev
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species_reconfigured
ssi-dk/MMASeq:species_reconfigured
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Commits
Commits on Jul 3, 2026
Add CPO.yaml configuration
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8502113
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Refactor E_coli.yaml configuration for tools
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Refactored E_Faecium.yaml configuration settings
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Refactored E_Faecalis.yaml configuration settings
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Correct species name casing in E_Faecium.yaml
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New species
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Merge branch 'dev' into species_reconfigured
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Merge branch 'spec_local' into species_reconfigured
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Commits on Jul 20, 2026
Added retries for curl when failing
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Splitted klebsiella in oxytoca and pneumoniae since it amrfinderplus support those individually
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Fixed errors in the configs
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Added spades to shovill env to avoid crash
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Commits on Jul 21, 2026
Small fix to blastn rule to have a header and wrangle better the final output
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Merge branch 'species_reconfigured' of https://github.com/ssi-dk/MMASeq into species_reconfigured
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Fix correct preset for K.oxytoca in kleborate
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Commits on Jul 27, 2026
Changed envs for Vanco fetch rules
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