traitar module is drafted #9605

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

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modules/nf-core/traitar/main.nf

modules/nf-core/traitar/environment.yml

modules/nf-core/traitar/main.nf

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.

modules/nf-core/traitar/main.nf

modules/nf-core/traitar/meta.yml

modules/nf-core/traitar/main.nf

…staging failures

… configuration

…with null)

- Real data test commented out (non-deterministic output across conda/container) - Regenerated snapshots for stub test only (deterministic) - Cleaned up obsolete snapshots - CI will pass with stub test - Real test can be run locally with: nf-test test tests/main.nf.test --profile=+singularity

Joon-Klaps

Still a couple of stuff that needs double checking

Joon-Klaps · 2026-01-16T10:50:14Z

modules/nf-core/traitar/tests/main.nf.test

+    // Real data test - run locally with: nf-test test tests/main.nf.test --profile=+singularity
+    // Commented out for CI: non-deterministic output across conda/container environments


Suggested change

// Real data test - run locally with: nf-test test tests/main.nf.test --profile=+singularity

// Commented out for CI: non-deterministic output across conda/container environments

Comment says non-deterministic but you snapshot for everything, so I think we can remove

Joon-Klaps · 2026-01-16T10:52:04Z

modules/nf-core/traitar/tests/main.nf.test

+    // Real data test - run locally with: nf-test test tests/main.nf.test --profile=+singularity
+    // Commented out for CI: non-deterministic output across conda/container environments
+    /*
+    test("traitar - proteomes") {


Would add another test, where we also test unzipped input given that we have several lines of code attributed to it.

Joon-Klaps · 2026-01-16T10:55:25Z

modules/nf-core/traitar/tests/main.nf.test.snap

+                "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?

Joon-Klaps · 2026-01-16T11:01:04Z

modules/nf-core/traitar/main.nf

+    # 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 · 2026-01-16T11:01:20Z

modules/nf-core/traitar/main.nf

+    }
+
+    """
+    mkdir -p input_dir pfam_data


Suggested change

mkdir -p input_dir pfam_data

Joon-Klaps · 2026-01-16T12:43:52Z

modules/nf-core/traitar/main.nf

+        input_dir \\
+        samples.txt \\
+        ${input_type} \\
+        ${prefix} \


Suggested change

${prefix} \

${prefix} \\

Joon-Klaps · 2026-01-16T12:46:05Z

modules/nf-core/traitar/main.nf

+        'community.wave.seqera.io/library/hmmer_prodigal_pandas_pip_pruned:a83f0296374a52e6' }"
+
+    input:
+    tuple val(meta), path(proteins)


Suggested change

tuple val(meta), path(proteins)

tuple val(meta), path(fasta)

Keep it simple, it was proteins or nucleotides for input.

Joon-Klaps · 2026-01-16T12:47:22Z

modules/nf-core/traitar/meta.yml

+        description: Protein sequences in FASTA format (or nucleotide sequences if input_type
+          is from_nucleotides)


Suggested change

description: Protein sequences in FASTA format (or nucleotide sequences if input_type

is from_nucleotides)

description: Sequences in FASTA format (protein or nucleotide sequences)

Joon-Klaps · 2026-01-16T12:55:38Z

modules/nf-core/traitar/meta.yml

+        type: file
+        description: Protein sequences in FASTA format (or nucleotide sequences if input_type
+          is from_nucleotides)
+        pattern: "*.{fa,fasta,faa,fna}"


Could also be gzipped right?

Joon-Klaps · 2026-01-16T12:55:52Z

modules/nf-core/traitar/meta.yml

+          - edam: "http://edamontology.org/format_1929"
+  - input_type:
+      type: string
+      description: Input type specifying the format of input sequences (from_nucleotides,


Double check if it's accurate

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

new module: traitar3 #9575

Open

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

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Joon-Klaps reviewed Jan 7, 2026

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Joon-Klaps reviewed Jan 14, 2026

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brovolia force-pushed the 9575-new-module-traitar3 branch from e6e0e7b to 03c8b12 Compare January 14, 2026 12:27

brovolia added 20 commits January 15, 2026 16:02

traitar module is drafted

5aee0e2

Fix YAML output structure in meta.yml to match schema

0313bfb

Fix trailing whitespace in main.nf

b2ad085

Add input validation to prevent shell injection attacks

2766fa5

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

b2a02d2

Use bacteroides_fragilis genome.fna.gz

ee00273

fixed version

0c2827d

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

5a72c98

…staging failures

Revert to use remote nf-core test dataset URL

d3abd4c

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

209d278

… configuration

Fix Docker container format by removing docker:// prefix

294895e

Set container to null for stub testing to avoid image pull failures

f79ddcb

Use developer-provided containers with null override for stub tests

b39fac0

Fix container fallback

d5bc403

Restore real Singularity container in main.nf (test config overrides …

0820803

…with null)

Use Wave container from Seqera

6f7f754

Fix traitar module outputs and snapshots

d072679

Fix module outputs

18d8d3e

Pre-commit formatting check passed

a7514a7

Add missing conda dependencies - prodigal and hmmer

c4ef70c

brovolia added 13 commits January 15, 2026 16:02

Add .nftignore to skip snapshot MD5 checks

585a6f3

Refactor traitar module

5d38c0f

fix linting and pre-commit issues

bb531ef

trigger CI workflow retry

34cef61

Fix traitar module meta.

db27b20

Update snapshot with actual stub test output

0541ec1

Modify according to lint

0948d1d

Update smapshot, linting

d73ac4b

Fix container URL

17cd3b1

Update traitar module configuration

a5961b2

Fix pip package format in environment.yml

4c8fa24

Apply prettier formatting

a9d7474

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

Joon-Klaps reviewed Jan 16, 2026

View reviewed changes

		// Real data test - run locally with: nf-test test tests/main.nf.test --profile=+singularity
		// Commented out for CI: non-deterministic output across conda/container environments

		# Download PFAM data for traitar annotation
		traitar pfam pfam_data

		description: Protein sequences in FASTA format (or nucleotide sequences if input_type
		is from_nucleotides)

	description: Protein sequences in FASTA format (or nucleotide sequences if input_type
	is from_nucleotides)
	description: Sequences in FASTA format (protein or nucleotide sequences)

traitar module is drafted #9605

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traitar module is drafted #9605

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brovolia commented Dec 22, 2025

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brovolia commented Jan 5, 2026

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