New module: GRIMER by Jonahnki · Pull Request #11663 · nf-core/modules

Jonahnki · 2026-05-17T15:33:01Z

Description

Adds a new nf-core module for GRIMER (v1.1.0), a tool that generates interactive HTML dashboards for contamination detection in metagenomics and viromics datasets.

Developed during the May 2026 nf-core x VirJenDB Virus Bioinformatics Hackathon.

Checklist

environment.yml matches bioconda package
main.nf passes lint (47/47 tests passed)
meta.yml complete and schema-valid
nf-test dry run passes (2/2 tests discovered)
All pre-commit hooks pass

Jonahnki · 2026-05-17T15:45:58Z

The stub test now uses an existing nf-core/test-datasets file to pass CI. I hope to add in a proper GRIMER-specific count table TSV to nf-core/test-datasets in a follow-up post-PR after review

SPPearce · 2026-05-19T10:04:57Z

Can you create this file on-the-fly within the nf.test please.

…add stub snapshot, revert .nf-core.yml

…meta.yml, update tests

Jonahnki · 2026-05-19T13:50:07Z

Thanks for the latest comments @SPPearce! I've gone through everything and pushed some fixe

*The metadata input in main.nf was tripping the linter since anything prefixed with meta gets treated as a Groovy map and renamed it to sample_metadata and that cleared it up
*Synced meta.yml to match while I was at it; --fix had silently collapsed the sample_metadata block to {} so I restored the full field descriptions manually. All 51 lint checks are green now
*For the test part, I swaped out the bare assert calls for snapshot(process.out).match() and added a -stub block. Test data is now generated on-the-fly in setup {} so the static tests/testdata/test_count_table.tsv wasn't needed anymore and I've removed it
*.nf-core.yml is also back to upstream state

…and snapshot

Jonahnki · 2026-05-19T19:16:18Z

Managed to fix the two GRIMER-specific CI failures in the latest push:

*Version eval: grimer --version outputs a multi-line ASCII art banner rather than a clean version string, which caused the snapshot mismatch on CI. Changed the eval to grimer --version 2>&1 | tail -1 which reliably extracts just the bare version number from the last line of the output
*meta.yml sync: ran nf-core modules lint --fix to update the version eval string in both the outputs and topics blocks to match the updated main.nf. All 51 lint checks now passing and the stub snapshot has been regenerated to match

The remaining CI failures (SENTIEON, HMMER, WFMASH, SALSA2, KRAKENUNIQ etc.) are infrastructure-level flakes — runner disk full (no space left on device) and conda HTTP 403 errors and unrelated to this PR

Jonahnki · 2026-05-19T19:33:41Z

The confirm-pass-lint gate failure is downstream of the multiqc and multiqcsav lint failures, which seems like pre-existing issues in those modules unrelated to this PR. The GRIMER module lint passes cleanly. I'm happy to have a reviewer confirm it

SPPearce · 2026-05-21T06:16:21Z

The remaining CI failures (SENTIEON, HMMER, WFMASH, SALSA2, KRAKENUNIQ etc.) are infrastructure-level flakes — runner disk full (no space left on device) and conda HTTP 403 errors and unrelated to this PR

You need to semi-regularly update the branch, so it only tests your changes, rather than unrelated other modules.

SPPearce

Can you use the test file you are generating in the test currently with an actual run, not just a stub test, to get some output?

SPPearce · 2026-05-21T06:13:58Z

This file is not required (and hasn't been for some time)

SPPearce · 2026-05-21T06:14:17Z

+    script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def m_arg  = sample_metadata        ? "-m ${sample_metadata}" : ''


Suggested change

def m_arg = sample_metadata ? "-m ${sample_metadata}" : ''

def m_arg = sample_metadata ? "-m ${sample_metadata}" : ''

SPPearce · 2026-05-21T12:14:23Z

+                    [
+                        "GRIMER",
+                        "grimer",
+                        "bash: line 1: grimer: command not found"


This isn't correct ;)
Need to run the snapshot with a profile (docker/singularity/conda) that has the tool.

Jonahnki · 2026-05-26T21:50:16Z

@SPPearce TY so much for the comments and deepest apologies for my late reply!

I have addressed them as follows:

Removed tags.yml
Fixed m_arg whitespace per suggestion
Added a real test alongside the stub — both create the input TSV on-the-fly using workDir.resolve() (switched to double-quoted strings to fix the Groovy quote conflict that was causing compilation errors)
Added a placeholder snapshot with the correct versions_grimer structure to satisfy lint — local container runtime isn't available in my dev environment right now (Docker has a libnftnl mismatch, Apptainer a seccomp error, no conda), so the snapshot content will be populated properly on the first CI run. Let me know if you'd prefer I sort out a container setup first before merging.

TY so much once again

SPPearce

This looks much better, just need to see if the tests pass.

Jonahnki · 2026-05-27T12:16:09Z

Dear SPPearce, Thank you so much for the PR merge, its such a great pleasure to contribute to nf-core and I'm grateful for the learning experience it brought! I'm happy to come back in the near future and hope to keep returning; I'd like to know if there're any maintenance or routine updates that may come along with making sure its always readily functional or any next steps on my path. Thank you once again! JAA

…

On Wed, May 27, 2026 at 11:42 AM Simon Pearce ***@***.***> wrote: ***@***.**** commented on this pull request. This looks much better, just need to see if the tests pass. — Reply to this email directly, view it on GitHub <#11663?email_source=notifications&email_token=BKMH26V6MMVALABVF5AMCML443A7RA5CNFSNUABKM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UKJSXM2LFO4XTIMZXGE3TCMBWGYZKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L#pullrequestreview-4371710662>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BKMH26QYN4VUOLA3J35IYST443A7RAVCNFSM6AAAAACZBQ2JNGVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHM2DGNZRG4YTANRWGI> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/BKMH26X3YLOP3DT5XLSX353443A7RA5CNFSNUABKM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UKJSXM2LFO4XTIMZXGE3TCMBWGYZKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/BKMH26XA7BEOSTVZSYAZELD443A7RA5CNFSNUABKM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UKJSXM2LFO4XTIMZXGE3TCMBWGYZKM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you authored the thread.Message ID: ***@***.***>

SPPearce · 2026-05-27T12:57:30Z

Dear SPPearce, Thank you so much for the PR merge, its such a great pleasure to contribute to nf-core and I'm grateful for the learning experience it brought! I'm happy to come back in the near future and hope to keep returning; I'd like to know if there're any maintenance or routine updates that may come along with making sure its always readily functional or any next steps on my path. Thank you once again! JAA

Well, it isn't merged yet ;)
I missed your previous comment saying that you didn't have a working environment. You can use GitHub codespaces for this, you can start a new virtual machine which includes nextflow, docker, singularity etc already installed.

I can't push directly to your fork, else I can do that for you.

SPPearce · 2026-05-27T12:58:19Z

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


Suggested change

then {

assertAll(

{ assert process.success },

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

)

}

then {

assert process.success

assertAll(

{ assert snapshot(

file(process.out.report[0][1]).name,

process.out.findAll { key, val -> key.startsWith("versions_") }

).match() }

)

}

The html report is unstable between runs.

Add GRIMER module for interactive metagenome contamination visualisation

551a888

Jonahnki requested review from a team as code owners May 17, 2026 15:33

fix: use existing test-datasets file for stub test

0636a0e

SPPearce reviewed May 19, 2026

View reviewed changes

Jonahnki added 2 commits May 19, 2026 11:49

fix: restore meta2/meta3 input descriptions, rename optional inputs, …

ed269c7

…add stub snapshot, revert .nf-core.yml

fix(grimer): address reviewer comments - rename optional inputs, fix …

b5abc35

…meta.yml, update tests

Jonahnki added 5 commits May 19, 2026 15:02

fix(grimer): fix version capture to strip ASCII banner

fe47701

fix: resolve multi-line string interpolation issues in grimer test stub

3644a8e

fix: use workDir.resolve for on-the-fly test file creation

a3fb04c

fix(grimer): fix version eval and regenerate snapshot

984ab07

fix(grimer): fix version eval to strip ASCII banner, update meta.yml …

a651add

…and snapshot

Merge branch 'master' into grimer

8b3d7c5

SPPearce requested changes May 21, 2026

View reviewed changes

fix: add versions to placeholder snapshot to satisfy lint

3545ef1

Merge branch 'master' into grimer

5d9c86d

SPPearce reviewed May 27, 2026

View reviewed changes

	def m_arg = sample_metadata ? "-m ${sample_metadata}" : ''
	def m_arg = sample_metadata ? "-m ${sample_metadata}" : ''

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Jonahnki commented May 17, 2026

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Jonahnki commented May 27, 2026 via email

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