traitar module is drafted by brovolia · Pull Request #9605 · nf-core/modules

brovolia · 2025-12-22T14:03:36Z

This module runs Traitar3 in phenotype mode to infer phenotype profiles from assembled nucleotide FASTA files, producing tabular trait prediction results per sample.

Copilot

Pull request overview

This PR adds a new nf-core module for Traitar3, which performs phenotype prediction from assembled nucleotide FASTA files using protein families to infer microbial traits.

Implements Traitar3 phenotype mode for trait prediction
Provides both script and stub implementations for testing
Includes comprehensive test configurations and expected outputs

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
modules/nf-core/traitar/main.nf	Core process implementation with Traitar3 phenotype analysis, including script and stub sections for prediction outputs
modules/nf-core/traitar/meta.yml	Module metadata defining inputs/outputs, tool information, and EDAM ontology annotations
modules/nf-core/traitar/environment.yml	Conda environment specification pinning traitar to version 3.0.1
modules/nf-core/traitar/tests/main.nf.test	nf-test implementation with stub test for proteome input
modules/nf-core/traitar/tests/main.nf.test.snap	Test snapshot file with expected MD5 checksums for stub outputs
modules/nf-core/traitar/tests/nextflow.config	Test-specific Nextflow configuration for module execution
modules/nf-core/traitar/tests/nf-test.config	Additional nf-test configuration settings
modules/nf-core/traitar/tests/config/nf-test.config	Alternative test configuration file for different test scenarios

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

brovolia · 2026-01-05T11:01:45Z

Hi @rpetit3 could you please review the module? :)

Joon-Klaps

Hi @brovolia,

Thanks for contributing Traitar3. I've left a couple of comments but they don't adress everything.

I've noticed that there are some files that shouldn't be there, .nftignore, nf-test.config, config/, ... All this are typicall for pipelines but not within nf-core modules.

I also noticed that the main.nf contains a bit of complexity and bash scripting, try to minimize this as much as possible. If you are struggeling decompressing files, there are plenty of examples already out there that resolve this issue, see this search

I would suggest having a read through the docs on does and don'ts of nf-core modules. I would also suggest to have a look at some already made modules like samtools/stats or trimgalore to get an idea of how the modules are structured.

Joon-Klaps

Still a couple of stuff that needs double checking

Joon-Klaps · 2026-01-16T10:55:25Z

+                "gene_prediction": [
+
+                ],
+                "pfam_annotation": [
+
+                ],


I'm not familar with traitar, is there an easy way to have output files for these variables, by adding more tests?

When I test the real data, the output turns out to be non-deterministic, so the md5 sums will be different. Will it work if I add content to stub files?

mmh That's then tricky..., depending on which files, you can try and see if there plugins available that facilitates deterministic regions from the files: https://plugins.nf-test.com/.

If there aren't any plugins and you cannot check for specific constant stings in the files. You can just snapshot the outputfile name. In the docs, we've written a few examples down on it. https://nf-co.re/docs/contributing/nf-test/assertions#complex---handling-inconsistent-md5sum-in-output-elements

Joon-Klaps · 2026-01-16T11:01:04Z

+    # Download PFAM data for traitar annotation
+    traitar pfam pfam_data


These should be given as an input variable; create a new module for it.

Have a look at nextclade/get_dataset as an example. Snapshotting both the db version as well as traitar is best practice.

For testing this module, you can use the downloaded one or use the one from nf-core/testdatasets (look for pfam)

Joon-Klaps

Almost there

Joon-Klaps · 2026-02-05T10:22:32Z

+    "versions": {
+        "content": [
+            null,
+            null
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2026-01-29T09:38:08.995821451"
+    },


Think this is an artifcat of previous tests?

Suggested change

"versions": {

"content": [

null,

null

],

"meta": {

"nf-test": "0.9.3",

"nextflow": "25.10.0"

},

"timestamp": "2026-01-29T09:38:08.995821451"

},

Joon-Klaps · 2026-02-05T10:24:20Z

Preferably, don't edit this file in this PR. If you would like to patch this, make a seperate PR and ask people of infrastructure on slack to have a look at it.

Joon-Klaps · 2026-02-05T10:35:55Z

+  - pfam_db:
+      type: directory
+      description: |
+        PFAM database directory created by traitar/pfamget module


Suggested change

PFAM database directory created by traitar/pfamget module

PFAM database directory created by traitar/pfamget module or downloaded from https://ftp.ebi.ac.uk/pub/databases/Pfam/

Joon-Klaps · 2026-02-05T10:39:03Z

I see in your commit history, the classic fight with linters & prettier is happening. Have a read here how to set it up.
https://nf-co.re/docs/contributing/code_editors_and_styling/code_formatting

…staging failures

… configuration

Joon-Klaps

Sorry 2 morte things that I overlooked, delete the code remenant in pfamget and undo any changes in .precommit-config.yaml please.

Joon-Klaps · 2026-02-11T13:24:05Z

Took the liberty to modify it myself, Awesome work.

brovolia · 2026-02-11T13:54:50Z

Yey! Thank you! You wrote me about .precommit-config.yaml, but I overlooked this file. Is there any documentation about it? I haven't touched these settings, so I have no idea, why there would be some changes.
So, can I merge the branch?

Joon-Klaps · 2026-02-11T14:04:58Z

YUP go ahead and merge, you deserve it!

There aren't any specific docs on not editing precommit.config.yaml. Generally, within a pull request, we focus on a single topic (e.g., creating a new module). We don't want to edit anything else.

I'm guessing if you didn't, an AI agent did.

brovolia linked an issue Dec 22, 2025 that may be closed by this pull request

new module: traitar3 #9575

Closed

4 tasks

brovolia self-assigned this Dec 22, 2025

brovolia requested a review from Copilot December 22, 2025 14:04

Copilot started reviewing on behalf of brovolia December 22, 2025 14:04 View session

brovolia requested a review from rpetit3 December 22, 2025 14:04

Copilot AI reviewed Dec 22, 2025

View reviewed changes

Comment thread modules/nf-core/traitar/main.nf Outdated

Comment thread modules/nf-core/traitar/environment.yml Outdated

Comment thread modules/nf-core/traitar/run/main.nf

Joon-Klaps reviewed Jan 7, 2026

View reviewed changes

Comment thread modules/nf-core/traitar/main.nf Outdated

Comment thread modules/nf-core/traitar/main.nf Outdated

Comment thread modules/nf-core/traitar/run/main.nf

Comment thread modules/nf-core/traitar/meta.yml Outdated

Comment thread modules/nf-core/traitar/main.nf Outdated

Joon-Klaps reviewed Jan 14, 2026

View reviewed changes

Comment thread modules/nf-core/traitar/main.nf Outdated

Comment thread modules/nf-core/traitar/main.nf Outdated

Comment thread modules/nf-core/traitar/main.nf Outdated

brovolia force-pushed the 9575-new-module-traitar3 branch 2 times, most recently from 890405a to a9d7474 Compare January 15, 2026 15:03

Joon-Klaps reviewed Jan 16, 2026

View reviewed changes

brovolia force-pushed the 9575-new-module-traitar3 branch 2 times, most recently from e6d796e to 12946f6 Compare January 29, 2026 14:43

brovolia requested review from a team as code owners January 29, 2026 14:43

brovolia force-pushed the 9575-new-module-traitar3 branch from 12946f6 to 273be60 Compare February 4, 2026 15:47

github-actions Bot added the size/l label Feb 4, 2026

Joon-Klaps reviewed Feb 5, 2026

View reviewed changes

brovolia added 10 commits February 10, 2026 11:41

traitar module is drafted

064eb31

Fix YAML output structure in meta.yml to match schema

2d532ae

Fix trailing whitespace in main.nf

f41bca1

Add input validation to prevent shell injection attacks

6304b0c

Update versions output to use topic-based format and fix meta.yml

5406b41

Use bacteroides_fragilis genome.fna.gz

5064f86

fixed version

2653051

Use simple local test file instead of remote dataset URL to avoid CI …

e9e6458

…staging failures

Revert to use remote nf-core test dataset URL

b6914ab

Use params.modules_testdata_base_path for proper nf-core test dataset…

d624781

… configuration

brovolia added 16 commits February 10, 2026 11:42

Update snapshot with actual stub test output

45d387d

Modify according to lint

a3dba1c

Update smapshot, linting

ff1e390

Fix container URL

e810b05

Update traitar module configuration

67571ba

Fix pip package format in environment.yml

681c258

Apply prettier formatting

be92c9c

Updated container to include parallel,fix comments

c17aefd

Fix linting,proteomes part

b1d7326

linting,container

adbc456

pre-commit fixing

1cb75ce

Refactor traitar module into pfamget and run

4f87e83

fix pre-commit

6090bdd

Update pre-commit config and prettier formatting

36e9de3

fixed md5 problem

50b7651

fix: remove input parameter

7ca2f90

brovolia force-pushed the 9575-new-module-traitar3 branch from 273be60 to 7ca2f90 Compare February 10, 2026 10:42

Joon-Klaps requested changes Feb 11, 2026

View reviewed changes

Comment thread modules/nf-core/traitar/pfamget/main.nf Outdated

Update modules/nf-core/traitar/pfamget/main.nf

a5d40b5

Joon-Klaps approved these changes Feb 11, 2026

View reviewed changes

Comment thread .pre-commit-config.yaml Outdated

Comment thread .pre-commit-config.yaml Outdated

Joon-Klaps added 2 commits February 11, 2026 14:23

Update .pre-commit-config.yaml

368b344

Update .pre-commit-config.yaml

9fcf256

Merge branch 'master' into 9575-new-module-traitar3

184766d

brovolia added this pull request to the merge queue Feb 11, 2026

Merged via the queue into master with commit 71ad2f5 Feb 11, 2026
32 checks passed

brovolia deleted the 9575-new-module-traitar3 branch February 11, 2026 14:53

		# Download PFAM data for traitar annotation
		traitar pfam pfam_data

	PFAM database directory created by traitar/pfamget module
	PFAM database directory created by traitar/pfamget module or downloaded from https://ftp.ebi.ac.uk/pub/databases/Pfam/

Conversation

brovolia commented Dec 22, 2025

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Uh oh!

Uh oh!

Uh oh!

brovolia commented Jan 5, 2026

Uh oh!

Joon-Klaps left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Joon-Klaps left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Joon-Klaps Jan 16, 2026

Choose a reason for hiding this comment

Uh oh!

brovolia Jan 26, 2026

Choose a reason for hiding this comment

Uh oh!

Joon-Klaps Jan 26, 2026

Choose a reason for hiding this comment

Uh oh!

Joon-Klaps Jan 16, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Joon-Klaps left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Joon-Klaps Feb 5, 2026

Choose a reason for hiding this comment

Uh oh!

Joon-Klaps Feb 5, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Joon-Klaps Feb 5, 2026

Choose a reason for hiding this comment

Uh oh!

Joon-Klaps commented Feb 5, 2026

Uh oh!

Joon-Klaps left a comment • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Joon-Klaps commented Feb 11, 2026

Uh oh!

brovolia commented Feb 11, 2026

Uh oh!

Joon-Klaps commented Feb 11, 2026

Uh oh!

Joon-Klaps left a comment •

edited

Loading