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12306 adding request db module to the nf coregapseq#12333

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12306-adding-request-db-module-to-the-nf-coregapseq
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12306 adding request db module to the nf coregapseq#12333
brovolia wants to merge 3 commits into
masterfrom
12306-adding-request-db-module-to-the-nf-coregapseq

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@brovolia

@brovolia brovolia commented Jul 9, 2026

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New submodule should provide a one-off download of db for gapseq, that the parallel processes can share it afterwards

@brovolia brovolia linked an issue Jul 9, 2026 that may be closed by this pull request
@github-actions github-actions Bot added the size/m label Jul 9, 2026

@dialvarezs dialvarezs left a comment

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Is it possible to integrate the output form the new GAPSEQ_REQUESTDB module into the other modules instead of just leaving the parameter empty?
That would help to test the wiring.

@brovolia

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I did this in the stub tests, so the wiring is validated with zero network cost. The real-data tests keep input[1] = [], so both the "shared pre-downloaded DB" and "self-download" paths are covered.

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Adding request db module to the nf-core/gapseq

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