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

README.md

@@ -1,4 +1,5 @@
 # ![nfcore/test-datasets](docs/images/test-datasets_logo.png)
+
 Test data to be used for automated testing with the nf-core pipelines
 
 > ⚠️ **Do not merge your test data to `master`! Each pipeline has a dedicated branch (and a special one for modules)**
@@ -13,8 +14,8 @@ The principle for nf-core test data is as small as possible, as large as necessa
 
 nf-core/test-datasets comes with documentation in the `docs/` directory:
 
-01. [Add a new  test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
-02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
+1.  [Add a new test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
+2.  [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
 
 ## Downloading test data
 
@@ -36,3 +37,22 @@ git fetch
 For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging).
 
 [^1]: From [stackoverflow](https://stackoverflow.com/a/60846265/11502856)
+
+## Datasets for nf-core/proteinannotator
+
+### DIAMOND test data
+
+Created to support the DIAMOND blastp taxonomic classification integration in nf-core/proteinannotator ([PR #50](https://github.com/nf-core/proteinannotator/pull/50)), and to address a CI disk-exhaustion issue flagged during review.
+
+Source: Minimal NCBI taxonomy and RefSeq data subset needed to exercise `DIAMONDPREPARETAXA`, `DIAMOND_MAKEDB`, `DIAMOND_BLASTP`, and `NCBIREFSEQDOWNLOAD` without pulling full production-scale databases. The five accessions below were deliberately chosen from the real `other` category because together they produce genuine DIAMOND alignment.
+
+- `WP_031942563.1` -- tetracycline efflux MFS transporter Tet(B) [Transposon Tn10]
+- `WP_430799656.1` -- class D beta-lactamase OXA-1379 [medical waste metagenome]
+- `WP_148044478.1` -- phosphoethanolamine--lipid A transferase MCR-5.4 [hospital metagenome]
+- `WP_168247882.1` -- extended-spectrum class C beta-lactamase IDC-2 [sediment metagenome]
+- `WP_168247881.1` -- extended-spectrum class C beta-lactamase IDC-1 [sediment metagenome]
+
+- `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_prot.accession2taxid.gz`: minimal accession2taxid map for DIAMOND_MAKEDB
+- `mini_taxdump.tar.gz`: minimal NCBI taxdump for DIAMONDPREPARETAXA tests
+- `test_refseq.fasta`: minimal refseq protein fasta for DIAMOND_BLASTP

testdata/diamond/test_refseq.fasta

@@ -0,0 +1,32 @@
+>WP_031942563.1 tetracycline efflux MFS transporter Tet(B) [Transposon Tn10]
+MNSSTKIALVITLLDAMGIGLIMPVLPTLLREFIASEDIANHFGVLLALYALMQVIFAPWLGKMSDRFGRRPVLLLSLIG
+ASLDYLLLAFSSALWMLYLGRLLSGITGATGAVAASVIADTTSASQRVKWFGWLGASFGLGLIAGPIIGGFAGEISPHSP
+FFIAALLNIVTFLVVMFWFRETKNTRDNTDTEVGVETQSNSVYITLFKTMPILLIIYFSAQLIGQIPATVWVLFTENRFG
+WNSMMVGFSLAGLGLLHSVFQAFVAGRIATKWGEKTAVLLEFIADSSAFAFLAFISEGWLDFPVLILLAGGGIALPALQG
+VMSIQTKSHEQGALQGLLVSLTNATGVIGPLLFTVIYNHSLPIWDGWIWIIGLAFYCIIILLSMTFMLTPQAQGSKQETS
+A
+>WP_430799656.1 class D beta-lactamase OXA-1379 [medical waste metagenome]
+MNKYLALLILLVYSQVSMAESIRENKSWNEVFAQESVEGVFVLCKSSKNDCITNNKERALLAFIPASTFKIANALIALET
+GVVKSEHQIFKWGGEPRDMKQWEQDFTLRGAMQASAVPVFQQFAREIGEKRMQSYLGEFAYGNSNIDGGIDLFWLEGGLR
+ISAINQIGFLESLYENKLPISERNQLIVKDALISEATPAYLIRSKTGYTGIKGKIQPGIAWWVGWVEKGTEVYFFAFNMN
+IDNESKLPARKSIPTKIMQSEGVLNGS
+>WP_148044478.1 phosphoethanolamine--lipid A transferase MCR-5.4 [hospital metagenome]
+MRLSAFITFLKMRPQVRTEFLTLFISLVFTLLCNGVFWNALLAGRDSLTSGTWLMLLCTGLLITGLQWLLLLLVATRWSV
+KPLLILLAVMTPAAVYFMRNYGVYFDKAMLRNLMETDVREASELLQWRMLPYLLVAAVSVWWIARVRVLRTGWKQAVMMR
+SACLAGALAMISMGLWPVMDVLIPTLRENKPLRYLITPANYVISGIRVLTEQASSSADEAREVVAADAHRGPQEQGRRPR
+ALVLVVGETVRAANWGLSGYERQTTPELAARDVINFSDVTSCGTDTATSLPCMFSLNGRRDYDERQIRRRESVLHVLNRS
+DVNILWRDNQSGCKGVCDGLPFENLSSAGHPTLCHGERCLDEILLEGLAEKITTSRSDMLIVLHMLGNHGPAYFQRYPAS
+YRRWSPTCDTTDLASCSHEALVNTYDNAVLYTDHVLARTIDLLSGIRSHDTALLYVSDHGESLGEKGLYLHGIPYVIAPD
+EQIKVPMIWWQSSQVYADQACMQTHASRAPVSHDHLFHTLLGMFDVKTAAYTPELDLLATCRKGQPQ
+>WP_168247882.1 extended-spectrum class C beta-lactamase IDC-2 [sediment metagenome]
+MPRTESVPSKSLVVRTLLLVFACLFPMAVPAVEDTSRVRTTVDAAILPLMSQHDIPGMVVGLILDGQPYVVTYGVASKEA
+NVPVAEATLFEIGSVSKVFTATLAAYAQTTGKLSLDDHPGKYLPQLKGTPIDQATLLHLGTYTAGGLPLQFPDEVTGEVA
+VMDYFRNWTPLAPPGTRREYSNASPGLLGLVAASALDDDFATLMQSTVFPAFGMTDSFIHVPDRKMPDYAWGYRKDRPVR
+VNEGPLDEQAYGVKTTVSDLLRFVQANIDPSSLEPSMRRAVEATQVGYFRAGTLVQGLGWEKYPYPVSREWLLGGNAKEM
+LFDPQPAYRLTDQTAGERYLFNKTGSTGGFATYVAFVPARKIGIVMLANRSYPIPDRVEAAWIILEQLASGTDSN
+>WP_168247881.1 extended-spectrum class C beta-lactamase IDC-1 [sediment metagenome]
+MPRTESVPSKSLVVRTLLLVFACLFPMAVPAVEDSSRVRAAVDAAILPLMSQHDIPGMAVGLILDGQPYVVTYGVASKET
+NVPVAEATLFEIGSVSKVFTATLATYAQATGKLSLDDHPGKYLPHLKGAPIDQATLLHLGTYTAGGLPLQFPDEVTGEAA
+VMNYFRNWTPLAPPGTRREYSNASPGLLGVVAASALDDDFATLMQTTVFPAFGMTDSFIHVPDRKMPDYAWGYRKDRRVR
+VNEGPLDEQAYGVKTTVSDLLRFVQANIDPNSLEPSMRHAVEATQVGYFRAGTLVQGLGWEKYPYPVSREWLLGGNAKEM
+LFDPQPAYRLTDQTAGGQYLFNKTGSTGGFATYVAFVPARKIGIVMLANRSYPIPDRVEAAWMILEQLASGTDSN