New module: spoligotyper by duceppemo · Pull Request #13085 · nf-core/modules

duceppemo · 2026-10-05T02:42:25Z

PR checklist

New module for spoligotyper (bioconda, docs): in silico spoligotyping of the Mycobacterium tuberculosis complex from reads (single or paired-end) or assemblies. Besides the spoligotype (binary, octal, hexadecimal, SB number), it reports the species from regions of difference, the lineage (Coll et al. 2014 barcode), the livestock lineages (Zwyer et al. 2021) and the lineage 1 sublineages (Netikul et al. 2022). Outputs: a table, JSON, a PDF report and a MultiQC custom content file.

nf-core test data has no M. tuberculosis complex genome, so the tests check that the module runs on the SARS-CoV-2 genome and reads and writes its outputs ("MTBC not detected" is the expected result for these data).

nf-core modules lint spoligotyper: 61 tests passed, 0 warnings, 0 failed.

🤖 Generated with Claude Code

In silico spoligotyping of the M. tuberculosis complex from reads or assemblies, with species (regions of difference) and lineages. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

vagkaratzas

Blocking: the module still uses legacy biocontainers/depot containers; it needs a Seqera Wave build (nf-core modules containers create).
Blocking: the tests should snapshot sanitizeOutput(process.out) (with unstableKeys plus a stable check for unstable channels) instead of picking channels and file names; the paired-end test only snapshots versions.
Smaller points: use ${prefix} in the output paths, quote interpolated paths, and fix the meta.yml details (args_id, FASTQ/FASTA ontologies, "Optional" on the PDF).

Not run: G1 and G2. The PR's nf-core CI workflows (Run Linting, Run nf-test) have not run on the head commit and are waiting for maintainer approval (action_required), so there is no CI result to read. Please run nf-core modules lint spoligotyper and the tests with --profile +singularity; the PR description says the Singularity test was not run. G3 (nextflow lint) passes.

Diff 7.41/10 · Overall 7.41/10
nf-core-reviewer 0.3.0 / vagkaratzas-review (rubric v2) · claude-sonnet-5-5

vagkaratzas · 2026-10-23T19:52:45Z

+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/spoligotyper:0.9.0--pyhdfd78af_0' :
+        'quay.io/biocontainers/spoligotyper:0.9.0--pyhdfd78af_0' }"


The container still points to legacy biocontainers / depot.galaxyproject.org. Please build a Seqera Wave container with nf-core modules containers create spoligotyper, which also adds the containers: block to meta.yml and the .conda-lock/ files.

vagkaratzas · 2026-10-23T19:52:45Z

+    tuple val(meta), path("*_spoligotyping.txt")    , emit: tsv
+    tuple val(meta), path("*_spoligotyping.json")   , emit: json
+    tuple val(meta), path("*_spoligotyping.pdf")    , emit: pdf, optional: true
+    tuple val(meta), path("*_spoligotyping_mqc.json"), emit: multiqc


The output names are predictable (--sample ${prefix} gives ${prefix}_spoligotyping.*), so use ${prefix} instead of globs.

Suggested change

tuple val(meta), path("*_spoligotyping.txt") , emit: tsv

tuple val(meta), path("*_spoligotyping.json") , emit: json

tuple val(meta), path("*_spoligotyping.pdf") , emit: pdf, optional: true

tuple val(meta), path("*_spoligotyping_mqc.json"), emit: multiqc

tuple val(meta), path("${prefix}_spoligotyping.txt") , emit: tsv

tuple val(meta), path("${prefix}_spoligotyping.json") , emit: json

tuple val(meta), path("${prefix}_spoligotyping.pdf") , emit: pdf, optional: true

tuple val(meta), path("${prefix}_spoligotyping_mqc.json"), emit: multiqc

vagkaratzas · 2026-10-23T19:52:45Z

+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Reads (single-end or paired-end) or an assembly: spoligotyper detects the file type
+    def input = reads instanceof List && reads.size() == 2 ? "-r1 ${reads[0]} -r2 ${reads[1]}" : "-r1 ${reads}"


Quote the staged file names in case they contain spaces.

Suggested change

def input = reads instanceof List && reads.size() == 2 ? "-r1 ${reads[0]} -r2 ${reads[1]}" : "-r1 ${reads}"

def input = reads instanceof List && reads.size() == 2 ? "-r1 '${reads[0]}' -r2 '${reads[1]}'" : "-r1 '${reads}'"

vagkaratzas · 2026-10-23T19:52:45Z

+    spoligotyper \\
+        $args \\
+        $input \\
+        --sample ${prefix} \\


Same here: quote the prefix.

Suggested change

--sample ${prefix} \\

--sample "${prefix}" \\

vagkaratzas · 2026-10-23T19:52:45Z

+  - genotyping
+  - lineage
+tools:
+  - spoligotyper:


The tool is missing args_id: "$args".

vagkaratzas · 2026-10-23T19:52:45Z

+            e.g. [ id:'test', single_end:false ]
+      - "*_spoligotyping.pdf":
+          type: file
+          description: PDF report for quality assurance (not written with --no-pdf)


The PDF output is optional (optional: true in main.nf), so the description should say "Optional".

Suggested change

description: PDF report for quality assurance (not written with --no-pdf)

description: Optional PDF report for quality assurance (not written with --no-pdf)

vagkaratzas · 2026-10-23T19:52:45Z

+
+    // nf-core test data has no M. tuberculosis complex genome: these tests check that the module runs and
+    // writes its outputs ("MTBC not detected" is the expected result).
+    test("sarscov2 - fasta") {


Put a bare assert process.success before assertAll(...), as in the nf-core template (same for the other two tests).

vagkaratzas · 2026-10-23T19:52:45Z

+                { assert snapshot(
+                    file(process.out.pdf[0][1]).name,
+                    file(process.out.json[0][1]).name,
+                    process.out.multiqc,
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match() }


Do not hand-pick channels and file names. Snapshot sanitizeOutput(process.out) and list only the truly unstable channels (the PDF and the JSON with run information, if they change between runs) in unstableKeys. Give each exempted channel back a stable check in the same snapshot(...), e.g. .contains() on a line the tool always writes.

vagkaratzas · 2026-10-23T19:52:45Z

+            assertAll(
+                { assert process.success },
+                { assert path(process.out.tsv[0][1]).text.contains('fastq') },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }


This test only snapshots the versions, so the paired-end branch is not checked against its outputs. Use snapshot(sanitizeOutput(process.out, unstableKeys: [...])) with the same stable checks as above.

vagkaratzas · 2026-10-23T19:52:45Z

+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }


Wrap the output with sanitizeOutput.

Suggested change

{ assert snapshot(process.out).match() }

{ assert snapshot(sanitizeOutput(process.out)).match() }

vagkaratzas · 2026-10-23T20:05:06Z

CI only runs automatically for nf-core members. Please ask for a GitHub invitation in the nf-core Slack #github-invitations channel; once you've joined, CI will run on your next push.

Comment added by Claude

- Seqera Wave containers (nf-core modules containers create) instead of the legacy biocontainers/depot images, with the conda lock files - Tests snapshot sanitizeOutput(process.out) with unstableKeys for the json and pdf channels (they embed run timestamps), plus stable content checks on those channels; snapshot regenerated - ${prefix} in the output paths, quoted interpolated paths - meta.yml: args_id, FASTQ/FASTA ontologies on the input, 'Optional.' on the pdf output, ${prefix} output names nf-core modules lint: 79 passed, 0 warnings, 0 failed. nf-test passes with --profile docker and --profile singularity. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

github-actions · 2026-10-27T15:24:28Z

This PR exceeds the recommended size of 1000 lines. Please make sure you are NOT addressing multiple issues with one PR. Note this PR might be rejected due to its size.

duceppemo · 2026-10-27T15:27:36Z

Thanks for the review @vagkaratzas — all points addressed in 009a860:

Containers: switched to Seqera Wave builds via nf-core modules containers create (amd64/arm64 docker + singularity, conda lock files included).
Tests: all tests now snapshot sanitizeOutput(process.out, unstableKeys: ["json", "pdf"]) (those two outputs embed run timestamps), with stable content checks on the unstable channels; the paired-end test now covers the full output. Snapshot regenerated.
Smaller points: ${prefix} in the output paths, quoted interpolated paths, and the meta.yml fixes (args_id, FASTQ/FASTA ontologies on the input, "Optional." on the PDF).

Verified locally: nf-core modules lint spoligotyper passes (79 passed, 0 warnings, 0 failed), and nf-test passes with both --profile docker and --profile singularity.

The CI workflows may still need maintainer approval to run on this PR.

vagkaratzas · 2026-10-27T20:08:15Z

CI only runs automatically for nf-core members. Please ask for a GitHub invitation in the nf-core Slack #github-invitations channel; once you've joined, CI will run on your next push.

Comment added by Claude

@duceppemo can you do the above so you become a member of the nf-core organization, in order to have the tests on the ci run?

New module: spoligotyper

f9b335f

In silico spoligotyping of the M. tuberculosis complex from reads or assemblies, with species (regions of difference) and lineages. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

vagkaratzas requested changes Oct 23, 2026

View reviewed changes

Merge remote-tracking branch 'upstream/master' into spoligotyper

97aa82e

github-actions Bot added the size/m label Oct 27, 2026

github-actions Bot added size/xl and removed size/m labels Oct 27, 2026

	def input = reads instanceof List && reads.size() == 2 ? "-r1 ${reads[0]} -r2 ${reads[1]}" : "-r1 ${reads}"
	def input = reads instanceof List && reads.size() == 2 ? "-r1 '${reads[0]}' -r2 '${reads[1]}'" : "-r1 '${reads}'"

	description: PDF report for quality assurance (not written with --no-pdf)
	description: Optional PDF report for quality assurance (not written with --no-pdf)

	{ assert snapshot(process.out).match() }
	{ assert snapshot(sanitizeOutput(process.out)).match() }

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duceppemo commented Oct 5, 2026

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vagkaratzas commented Oct 23, 2026

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