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Fix centrifuger output naming to avoid filename collisions in taxprof…#11990

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haris18s:fix_names
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Fix centrifuger output naming to avoid filename collisions in taxprof…#11990
haris18s wants to merge 1 commit into
nf-core:masterfrom
haris18s:fix_names

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@haris18s

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Updates the output filenames of centrifuger/centrifuger and centrifuger/quantification to be distinct, so they don't collide when used in the same pipeline (e.g., nf-core/taxprofiler).

Changes:
centrifuger/centrifuger: output pattern changed from *.tsv to *.classification.tsv (script and stub updated accordingly)
centrifuger/quantification: Output pattern changed from hardcoded ${meta.id}.tsv to glob *.report.tsv so custom ext.prefix works correctly.

Both modules previously emitted ${prefix}.tsv, causing filename collisions when both were used together in a pipeline (e.g., centrifuger classification + quantification in nf-core/taxprofiler).

@jfy133

jfy133 commented Jun 15, 2026

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Actually this should not be necessary here - we can fix this in the pipelien with modules.conf :) (i.e. add .classification. via the ext.prefix bit :)

@jfy133

jfy133 commented Jun 15, 2026

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(e.g. maybe a differnet pipelline dev doesn't want .classificaiton in the name, but something else)

@haris18s

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Actually this should not be necessary here - we can fix this in the pipelien with modules.conf :) (i.e. add .classification. via the ext.prefix bit :)

ok thanks for letting me know, i thought would be more clear to have it in module-level,as centrfiuge has different names.
I reverted the "classification" / "report" suffix cchanges, but i replaced meta.id with *tsv. for flexibility

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2 participants