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Add DIAMOND blastp test fixtures (taxdump, accession2taxid map, refseq_fasta) - #2287

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tracelail merged 4 commits into
nf-core:proteinannotatorfrom
tracelail:proteinannotator
Sep 23, 2026
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tracelail merged 4 commits into
nf-core:proteinannotatorfrom
tracelail:proteinannotator

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@tracelail

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Adds test fixtures for the DIAMOND blastp integration in nf-core/proteinannotator#50:

test_refseq.fasta: minimal refseq protein fasta for DIAMOND_BLASTP
refseq/release/other/other.wp_protein_test.1.protein.faa.gz: minimal RefSeq 'other' category subset for NCBIREFSEQDOWNLOAD, replacing the full-category download that was exhausting CI disk space
mini_taxdump.tar.gz: minimal NCBI taxdump for DIAMONDPREPARETAXA tests
mini_prot.accession2taxid.gz: minimal accession2taxid map for DIAMOND_MAKEDB

All four verified locally against the pipeline's NCBIREFSEQDOWNLOAD module test, diamond subworkflow test, and functional_annotation subworkflow test. Full suite passes with real BLASTP output.

@erikrikarddaniel erikrikarddaniel left a comment

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We're supposed to have a README.md that describes the data: what it's for, how it was made etc. Otherwise this looks fine, so ping me when you've added that.

@vagkaratzas

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We're supposed to have a README.md that describes the data: what it's for, how it was made etc. Otherwise this looks fine, so ping me when you've added that.

Yes please. @tracelail feel free to init that README.md file and I'll append the rest of the already existing files which are not documented. You can get inspiration from other pipelines, such as metatdenovo

@tracelail

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@vagkaratzas, readme is initialized with the Diamond sections. Feel free to edit as you see fit.

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Removing duplicate naming and adding bullet points so items dont show in one line and should be fine. Feel free to merge after this small update

Comment thread README.md Resolved
Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
@tracelail
tracelail merged commit 7b2340c into nf-core:proteinannotator Sep 23, 2026
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3 participants