Feature/localcdsearch #9632

Ales-ibt · 2026-01-09T11:17:37Z

This PR contains the addition of the local-cd-search tool module (annotate and download). Please note that the tool version is not displayed in v0.3.0. I had opened an issue requesting the functionality to the original author. At the moment, the version is hardcoded.

Also, local-cd-search image is not available in Seqera Containers yet and Galaxy Depot doesn't have it either, so we are relying on biocontainers.

Thank you for reviewing!

PR checklist

Closes #9574

jfy133

Review for just download mostly what we talked about on Slack and then a few other minor things

modules/nf-core/localcdsearch/annotate/main.nf

modules/nf-core/localcdsearch/download/main.nf

modules/nf-core/localcdsearch/download/meta.yml

modules/nf-core/localcdsearch/annotate/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

vagkaratzas

Nice! Couple of things and it should be getting there

modules/nf-core/localcdsearch/download/main.nf

modules/nf-core/localcdsearch/annotate/main.nf

vagkaratzas · 2026-01-12T11:41:28Z

modules/nf-core/localcdsearch/download/main.nf

+        'biocontainers/local-cd-search:0.3.0--pyhdfd78af_0' }"
+
+    input:
+    val databases


If you ask me, I would add a meta since it's the only input, but don't really have a strong opinion for or against it. mmseqs_databases module is also not using any meta for val database which is also a single input.

Meta should be the database name, right? The problem with meta here is that the input is a list that can contain multiple databases. It sound to me that handling a list on meta will be problematic. The option would be to join the list into a string, but that would be hard to read

modules/nf-core/localcdsearch/download/main.nf

modules/nf-core/localcdsearch/download/tests/main.nf.test

modules/nf-core/localcdsearch/download/meta.yml

modules/nf-core/localcdsearch/annotate/main.nf

vagkaratzas · 2026-01-12T12:01:52Z

modules/nf-core/localcdsearch/annotate/tests/main.nf.test

+            process {
+                """
+                input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) ]
+                input[1] = LOCALCDSEARCH_DOWNLOAD.out.db


Just curious, if you had downloaded multiple dbs, would this still be the same? Or do you need to select one or more of the downloaded dbs somehow?

The downloader tool creates the databases directory structure and the annotator detects all the available databases in the given directory. Then the tool runs the annotation versus ALL the detected databases. There's no way to select which database to use when multiple databases exists

Updated version information to use a variable for better maintainability.

Added version information for the tool in the main.nf file.

Added version information to the main.nf file.

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

vagkaratzas

Two last comments and I think it's good to go

modules/nf-core/localcdsearch/annotate/tests/main.nf.test

modules/nf-core/localcdsearch/annotate/main.nf

vagkaratzas

Looks good IMO! Can always patch-update later if something's off!

* local-cd-search annotate and download modules * Fixing lint * Update localcdsearch tool metadata in meta.yml * Fix container URL selection logic in main.nf * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Fix container URL for local-cd-search * Update modules/nf-core/localcdsearch/annotate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Singularity container added * edamontology added * Updating test for one input only * Updating snap * Updating test for db downloding * Update version handling in main.nf * Update version expression in meta.yml * Refactor version handling in main.nf Updated version information to use a variable for better maintainability. * Update version retrieval expression in meta.yml * Add version information to stub Added version information for the tool in the main.nf file. * Add version information to stub Added version information to the main.nf file. * Update modules/nf-core/localcdsearch/download/meta.yml Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> * Refactor assertions to include process success check * Refactor assertions for process success in tests * Update container URL for local-cd-search * Remove redundant success assertion in tests --------- Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

Ales-ibt added 2 commits January 9, 2026 10:56

local-cd-search annotate and download modules

b3954d5

Fixing lint

895b307

Ales-ibt requested review from mberacochea and vagkaratzas January 9, 2026 11:17

Ales-ibt and others added 8 commits January 9, 2026 11:22

Merge branch 'master' into feature/localcdsearch

acd1f00

Update localcdsearch tool metadata in meta.yml

c344319

Fix container URL selection logic in main.nf

8b108c0

Fix container URL for local-cd-search

2ea6819

Fix container URL for local-cd-search

3bb7e77

Fix container URL for local-cd-search

a62d497

Fix container URL for local-cd-search

9c89f90

Fix container URL for local-cd-search

e4e0752

jfy133 reviewed Jan 9, 2026

View reviewed changes

SPPearce reviewed Jan 9, 2026

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modules/nf-core/localcdsearch/annotate/main.nf Outdated Show resolved Hide resolved

Ales-ibt and others added 16 commits January 9, 2026 13:28

Update modules/nf-core/localcdsearch/annotate/main.nf

a8e7d5c

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/main.nf

b7c1b43

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/main.nf

cd88e7f

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/main.nf

68fd0c8

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/main.nf

6fe433a

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/main.nf

b2a2fd9

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/main.nf

979823f

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/meta.yml

6366acd

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/meta.yml

59e6941

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update modules/nf-core/localcdsearch/download/meta.yml

3bee222

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Singularity container added

822536c

edamontology added

289b1af

Updating test for one input only

448a4ea

Updating snap

5426030

Updating test for db downloding

86024dc

Merge branch 'master' into feature/localcdsearch

c953ca8

Ales-ibt requested review from SPPearce and jfy133 January 9, 2026 14:39

Ales-ibt added 2 commits January 12, 2026 09:07

Merge branch 'master' into feature/localcdsearch

301780d

Merge branch 'master' into feature/localcdsearch

b9a6632

vagkaratzas requested changes Jan 12, 2026

View reviewed changes

Ales-ibt and others added 10 commits January 12, 2026 13:42

Update version handling in main.nf

2c803fd

Update version expression in meta.yml

2c329bb

Refactor version handling in main.nf

bf16933

Updated version information to use a variable for better maintainability.

Update version retrieval expression in meta.yml

8a6184a

Add version information to stub

64d0174

Added version information for the tool in the main.nf file.

Add version information to stub

2e368d7

Added version information to the main.nf file.

Merge branch 'master' into feature/localcdsearch

84f955a

Update modules/nf-core/localcdsearch/download/meta.yml

a75edc7

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>

Refactor assertions to include process success check

dd7c915

Refactor assertions for process success in tests

ede89e2

Ales-ibt requested a review from vagkaratzas January 12, 2026 14:48

Merge branch 'master' into feature/localcdsearch

6a5bb84

vagkaratzas requested changes Jan 12, 2026

View reviewed changes

modules/nf-core/localcdsearch/annotate/tests/main.nf.test Outdated Show resolved Hide resolved

modules/nf-core/localcdsearch/annotate/main.nf Outdated Show resolved Hide resolved

Ales-ibt added 2 commits January 12, 2026 15:59

Update container URL for local-cd-search

bf7db4d

Remove redundant success assertion in tests

0d9b181

Ales-ibt requested a review from vagkaratzas January 12, 2026 16:02

vagkaratzas approved these changes Jan 12, 2026

View reviewed changes

Ales-ibt added this pull request to the merge queue Jan 13, 2026

Merged via the queue into master with commit 04dcc4d Jan 13, 2026
52 checks passed

Ales-ibt deleted the feature/localcdsearch branch January 13, 2026 15:43

Feature/localcdsearch #9632

Feature/localcdsearch #9632

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Ales-ibt commented Jan 9, 2026 •

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