Hi, I've been tweeking the universc module and found out that the nf-test was failing for singularity because

--writable-tmpfs

doesn't seems to work with

underlay

WARNING: Disabling --writable-tmpfs as it can't be used in conjunction with underlay

Hence the executable

/cellranger-3.0.2.9001/cellranger

cannot be modify and universc script fail. It does work with Docker using

--privileged

. What would be the prefered way to solve this ? I was thinking of maybe copying the

/cellranger

folder in a temporary writable file when the module execute (does work on singularity but need to overwrite the

PATH

).

Would anyone want to volunteer to update the README.md in the modules repo? Specifically, the "images" (i.e. the example of the terminal output): They are really really old, and don't reflect the current nf-core output especially well

Might I be able to get a hand with an update to version 10.1.0 of cellranger? It appears the docker container process is manual, I don't believe I have write access to the Dockerhub nfcore organization github.com/nf-core/modules/…/cellranger#… (also posted in https://nfcore.slack.com/archives/CHN5BV5DW/p1789667275989939)

Moving a hardcoded argument in sourmash/sketch to an optional input (and then updating the tests of everything using it): https://github.com/nf-core/modules/pull/12999

Hi! Can someone please review this PR for tantan module. Thanks! https://github.com/nf-core/modules/pull/13017

Hi all! First-time contributor here, I've opened a PR adding a modkit/dmr module (thin wrapper around modkit dmr pair, for differential methylation between a pair of bedMethyl samples, haplotypes, tumor/normal, etc.): nf-core/modules#13021 It needs a companion test-data PR since there's no bedmethyl fixture in test-datasets yet (generated from the existing phased nanopore BAM modkit/pileup's own tests already use, so no new BAM/reference needed): nf-core/test-datasets#2289 Both are ready for review, happy to make changes if anything's off convention-wise. Thanks!

Can someone please review - bump

octopusv

submodules to 1.0.0 : github.com/nf-core/modules/pull/13046 (minor changes but looks huge only because of conda lock files and updated snapshots)

Hi everyone! I'm contributing nf-core modules for InstaNexus (on bioconda), starting with

instanexus/assemble

(nf-core/modules#13044). For its tests I'd like to add a small CSV (43 rows, 6.3 KB) to the modules branch of test-datasets: InstaNovo predictions on a BSA sample after InstaNexus preprocessing. The data are ours, published with the InstaNexus article in MCP (CC BY 4.0). Would

data/proteomics/instanexus/bsa_cleaned.csv

be the right place? The file is the output of the future

instanexus/preprocess

module, so once that's published we can switch the test to run it upstream instead. Thanks!

Hi! Here is an uneventful bump to latest Sniffles: github.com/nf-core/modules/pull/13093. I am sorry I missed what I should do about the PR size label... 👀 Can someone have a look?

Following up with a Sniffles genotyper module: github.com/nf-core/modules/pull/13105 which needs testdata: github.com/nf-core/test-datasets/pull/2302. If somebody helped me to merge testdata I could generate necessary snaps for tests in the module 🛠️☺️

Hi! I'm currently updating the chopper module. In the [documentation](github.com/wdecoster/chopper#…), it's advised to use pigz as a replacement for zcat + gzip. Since pigz is used twice in the module (once for decompressing, a second time for compressing output):

pigz \\
        -dc \\
        -p ${task.cpus} \\
        $args \\
        $fastq | \\
    chopper \\
        --threads $task.cpus \\
        $fasta_filtering \\
        $args2 | \\
    pigz \\
        -p ${task.cpus} \\
        $args3 > ${prefix}.fastq.gz

I need to define it twice in the meta yaml:

tools:
  - "pigz":
      description: "A parallel implementation of gzip for modern multi-processor, multi-core machines."
      documentation: "<https://zlib.net/pigz/>"
      args_id: "$args"
      identifier: ""
  - "chopper":
      description: "A rust command line for filtering and trimming long reads."
      homepage: "<https://github.com/wdecoster/chopper>"
      documentation: "<https://github.com/wdecoster/chopper>"
      tool_dev_url: "<https://github.com/wdecoster/chopper>"
      doi: "10.1093/bioinformatics/bty149"
      licence: ["MIT"]
      args_id: "$args2"
      identifier: ""
  - "pigz":
      description: "A parallel implementation of gzip for modern multi-processor, multi-core machines."
      documentation: "<https://zlib.net/pigz/>"
      args_id: "$args3"
      identifier: ""

The thing is, once the replacement of both zcat and gzip by pigz is done, I get an error with the linter:

main_nf_version_emit: Module does not have an emit: and topic: for each software version

In your opinion, how should I proceed? Thanks!

Hi everyone ! 😊 I’m adding a new nf-core module for kivvi and would need some advice on adding test data. The tool runs in two modes which require reads spanning specific genomic regions, that i don't think are covered by existing files in

nf-core/test-datasets

. There are available bams for both (kiv2 and d4z4) that are pretty small, could I just add these files to the test-datasets repo ?

Hello everyone I'm just open two module pull request for a plastic degrading enzyme prediction pipeline :: github.com/nf-core/modules/pulls?q=is%3Apr+state%3Aopen… it contain colabfod and tmalign module

In light of the upcoming hackathon, I've been clearing the nf-core/modules wishlist from already-completed items so they don't get in our way. For people joining the Agentic module development track, here is the shared doc/manual for our Team 😄 It includes preparation notes, tips, goals, and more. Advised to have a quick look before the Day. It also links to the shared spreadsheet upon which we will evaluate our bots efforts. This is where we write stuff as we prompt the agents (runs), and then evaluate them (reviews). Looking forward to this modules galore mayhem!!! See you all there.

WARNING; this channel is going to be spammed upon 15-16 OCT.

-> Mute at your own discretion.

alert For those interested in joining the module container conversion party party parrot, I created a tracking issue for modules with the conversion pending here. Make sure you create an issue from there (check image below to learn how) so that everything is automatically and properly linked 😉 (Also assign yourself to the issue you created!)

In order to work in parallel instead of against the @Marcel Ribeiro-Dantas + @mashehu team track above, I updated the github.com/vagkaratzas/nf-core-module-dev plugin (now v.1.6.0) to by default run

nf-core modules container create

, finally moving away from the bioconda/quay/galaxy container stack. You might want to

export TOWER_ACCESS_TOKEN (a free Seqera Platform token) in the shell you start the agent from

so you can have unlimited container builds for the hackathon - we will need it :D More happy news: Seqera's own Nextflow plugin for Claude/Codex is out: github.com/seqeralabs/nextflow-plugin ! Kudos to @Sasha Dagayev!! So I added a 5th test case in our evaluation board for tomorrow; a combination of the

nextflow-plugin

+ the nf-core/modules AGENTS.md. It would be unfair to test without the AGENTS.md, since the

nextflow-plugin

is not following nf-core standards as strictly as the

nf-core-module-dev

does. Instructions have been updated over at: docs.google.com/document/d/1AetwQUNt-tW…/edit?tab=t.0 Spreadsheet for our evaluation as well, accordingly: docs.google.com/spreadsheets/d/14oPqv-WXwYX…/edit?gid=0#gid=0 Sleep well, see you soon :D

More great news! You can now join the

agents nf-core modules evaluation

track even if you don't have a Claude or Codex subscription.

Seqera AI

got as covered for the hackathon: https://nfcore.slack.com/archives/C0BKZMG6467/p1792019303626159

First PR: github.com/nf-core/modules/pull/13171

Hue or Sidd review pliz: github.com/nf-core/modules/pull/13278

Back-to-back release (v1.7.0) for the

nf-core-module-dev

plugin, based on fixes/enhancements from the hackathon's agentic module evaluation track (15 runs, 13 PRs, 21 reviews). Changelog: github.com/vagkaratzas/nf-core-module-dev/…/1.7.0 Thank you all, and see you in the distributed one ;)

Next up, testing the

savvy-progress

mod (Claude only) inside

nf-core-module-dev

, adding the necessary instructions to use it if installed. So you can have a details/progress window for each subagent and the overall plan.

hey guys! i am trying to test out parabricks/starfusion and got an odd error:

usage: pbrun starfusion <options>
Help: pbrun starfusion -h
pbrun: error: unrecognized arguments: --num-gpus 1

this is not an option i added, it is hard-coded into the module when using gpu acceleration. seems like i have to use --num-threads 1 instead. it seems very odd to me if this is a real error and the module passed checks, and from what i can see it looks like it was configured to run on gpu runners. it also seems odd to me that this module hasn't been edited in a year without anyone noticing? just wondering if there's something wrong with my setup is all

Hi, I'm iraajgangavaram on GitHub. A maintainer asked me to join the nf-core GitHub org so CI runs on my celltypist module PR (nf-core/modules#13438). Could someone send me an invite? Thanks.

Hi, could someone merge nf-core/test-datasets#2350 when they have a moment? It's approved and the checks pass. The CellTypist module PR (#13438) needs these files for its tests. Thanks!

Hi, could someone take a look at nf-core/modules#13465 (new scdblfinder module)? I've addressed the review comments: the h5ad is written with gzip, and the predictions output is now a boolean-only CSV so it works with scdownstream's doublet removal. Checks are green. Thanks!

Hi all. I am trying to merge the module longphase/modcall, and prek seems to fail. It doesn't appear to be from my module, but from some subworkflows where the shebang seems to be off. More specifically, the error in the logs is; "Shebang comment should appear at the first line @ line 4, column 22" Maybe from pr #13448? If I am missing something on my end, let me know so I can fix it.

Asked this question on a closed pull request, so probably not likely to be answered there github.com/nf-core/modules/issues/13228#… What is the process for bumping a bioconda-based tool version with Seqera containers?

Hello, I have written a Nextflow module to support WormCat, a tool designed to help C. elegans researchers categorize and visualize gene set enrichment data. I am now working on the nf-test cases and need some advice on test data. I came across the nf-core test-datasets repository, but I was wondering whether it is acceptable to host my own test data or whether I should create a new branch in the nf-core/test-datasets repository. WormCat accepts CSV or Excel files as input. The CSV file must include a column header named

Sequence ID

or

Wormbase ID

(case-sensitive). Any advice would be appreciated. Thanks!

I received a bug report for minimap2/align bundled samtools command github.com/nf-core/genomeassembler/issues/265 and I am a bit surprised that this hasnt surfaced before, could someone who is into samtools take a quick look?

Hi @core-team / @modules-reviewers! 👋 When you have a moment, could someone please review/merge two new DSL2 modules that are fully green on CI? 1. spatialcontinuum: github.com/nf-core/modules/pull/13487 (28/28 checks green, Seqera Wave container tested) 2. insitugame: github.com/nf-core/modules/pull/13471 (17/17 checks green, Seqera Wave container tested) Both modules are verified with real biocontainers and pass all pytest-workflow tests. Thank you so much!