#1166 Add mindwell and mindwell_gpu profiles to vsc_kul_uhasselt Pull request opened by ljwharbers This is not a new config profile, but an extension of the existing

vsc_kul_uhasselt

config. KU Leuven's Tier-2 infrastructure gained a new cluster, Mindwell, alongside Genius and wICE. The

vsc_kul_uhasselt

config previously only knew

genius

,

genius_gpu

,

wice

,

wice_gpu

and

superdome

, so pipelines could not be steered to Mindwell at all. Changes Adds

mindwell

and

mindwell_gpu

sub-profiles, structurally identical to the existing

wice

/

wice_gpu

pair, plus two queue-selection closures (

determineMindwellQueue

,

determineMindwellGpuQueue

) that reuse the existing

limitTaskTime()

helper and the

VSC_DEDICATED_QUEUES

mechanism. Partition mapping (verified against

sinfo -M mindwell

and `scontrol -M mindwell show partition`; all Mindwell nodes have 192 cores): | Partition | Mem/node | MaxTime | Account | | -------------------------------- | ----------- | ------- | ------------------------ | | batch_graniterapids (default) | 768000 MB | 3 d | $SLURM_ACCOUNT | | batch_graniterapids_long | 768000 MB | 7 d | $SLURM_ACCOUNT | | bigmem | 1536000 MB | 3 d | $SLURM_ACCOUNT | | gpu_b200 (8× B200) | 1536000 MB | 3 d | $SLURM_ACCOUNT | | dedicated_big_bigmem | 1536000 MB+ | 7 d | lp_big_mindwell_cpu | | dedicated_big_gpu_b200 (8× B200) | 2313600 MB | 7 d | lp_big_mindwell_gpu_b200 | Notes: •

bigmem

and

gpu_b200

cap at 3 days, so those branches clamp

task.time

via

limitTaskTime()

, the same way

determineWiceQueue

already does. • GPU count defaults to

cores / 24

(192 cores ÷ 8 B200 per node) when

accelerator

is not set. • The dedicated partitions set

AllowAccounts=<their own account>

and every public partition sets

DenyQos=…,lp_big_mindwell_cpu,lp_big_mindwell_gpu_b200

, so partition and account are hard-locked; the profiles pick the account from the resolved queue. •

interactive

and

dedicated_afaa_bigmem

are deliberately not exposed. Docs additions cover the two Mindwell-specific hazards:

dedicated_big_bigmem

exists on both wICE and Mindwell but needs a different account on each, and

$VSC_SCRATCH

resolves to Lustre on wICE/Genius but GPFS on Mindwell — so a head job on the wrong cluster silently puts

NXF_WORK

and the container cache on the wrong filesystem. Testing •

nextflow config -profile mindwell

and

-profile mindwell_gpu

resolve, with

--clusters=mindwell

and the correct accounts in

clusterOptions

. • Routing closures exercised directly against the boundary values (below/at the 703 GB threshold, 72 h threshold, with and without each dedicated queue present), including the

task.time

clamping;

determineWiceQueue

/

determineGeniusQueue

verified unchanged. • Every queue the closures can return has a matching

cluster/mindwell/<partition>

Lmod module, so the existing

beforeScript

pattern works unchanged. •

prettier

and

editorconfig-checker

pre-commit hooks pass. No changes needed to

nfcore_custom.config

or

.github/workflows/main.yml

—

vsc_kul_uhasselt

is already registered there and only top-level profiles are enumerated. PR checklist • Your PR targets the

master

branch • Documentation updated in

docs/vsc_kul_uhasselt.md

• No new top-level profile, so

nfcore_custom.config

and the CI

profile:

scope are unchanged 🤖 Generated with Claude Code nf-core/configs

#1168 bump highmem threshold to 250GB and add bash login shell to all jobs Pull request opened by vsuppiyar Hi, I've made small changes to the currently existing

dkfz.config

file. I have updated the

highmem

queue threshold from 200 GB to 250 GB. Further, I made sure that the job starts in a bash login shell by adding

-L /bin/bash

to

clusterOptions

. Previously, jobs could default to

sh

, which sometimes failed to properly initialize the environment (e.g.

nextflow

not being on

PATH

), causing issues. In addition to that, I had to downgrade from

Nextflow/25.10.0

to

Nextflow/24.10.2

(available as cluster module) in the docs, otherwise you are running into this known issue. This is not a new profile.

dkfz

is already registered in

nfcore_custom.config

and

.github/workflows/main.yml

. @kubranarci @Abid Abrar. nf-core/configs

#1169 Add local executor resource limits to PDC KTH profile Pull request opened by mahesh-panchal Summary • Cap the

local

executor on the

pdc_kth

profile to 8 CPUs / 128GB memory, so processes marked to run locally (short jobs that don't go through Slurm) don't fan out and overburden the shared Dardel login node. nf-core/configs

#1170 Add local executor resource limits to Pelle profile Pull request opened by mahesh-panchal Summary • Cap the

local

executor on the

pelle

profile to 8 CPUs / 128GB memory, so processes marked to run locally (short jobs that don't go through Slurm) don't fan out and overburden the shared Pelle login node. nf-core/configs

#1171 Fix project fetching for tier1 Pull request opened by nvnieuwk Add logic to define the Scratch directory based on environment variable. --- name: New Config about: A new cluster config Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

scope in

.github/workflows/main.yml

• OPTIONAL: Add your custom profile path and GitHub user name to

.github/CODEOWNERS

(

**/<custom-profile>** @<github-username>

) nf-core/configs

#1172 update clusters and params.vsc_ugent_tier1_project + update docs Pull request opened by mvheetve • name: Update vsc_ugent.config • about: Update to our institutional hpc config. Clusters were outdated, one parameters was not declared correctly and the projct directory could not be found due to a missing 'return'. Docs updated accordingly. Tested using nf-core/rnaseq on both tier1 and tier2 clusters, without anything to report. Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

scope in

.github/workflows/main.yml

• OPTIONAL: Add your custom profile path and GitHub user name to

.github/CODEOWNERS

(

**/<custom-profile>** @<github-username>

) nf-core/configs

#1173 Configuration for Saga HPC, Sigma2.no Pull request opened by arupgsh --- name: Saga Sigma2.no about: A new cluster config Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

scope in

.github/workflows/main.yml

• OPTIONAL: Add your custom profile path and GitHub user name to

.github/CODEOWNERS

(

**/<custom-profile>** @<github-username>

) nf-core/configs

#1174 naiss profile, including support for arrhenius Pull request opened by pontus --- name: NAISS about: Profile to support naiss resources, starting with arrhenius hpc This is work-in-progress, please do not merge until confirmed working. Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

scope in

.github/workflows/main.yml

• OPTIONAL: Add your custom profile path and GitHub user name to

.github/CODEOWNERS

(

**/<custom-profile>** @<github-username>

) nf-core/configs

#1175 Remove 'scratch' option from executor Cambridge configuration Pull request opened by RaqManzano Removed the 'scratch' option from the executor configuration. We have discovered though usage that

scratch

option is not working well for our cluster as the default

tmp

gets full quite easily. Therefore I am removing this option from the config, users can still activate it through their config if they wish to. nf-core/configs

#1176 purdue_gautschi & purdue_negishi: add apptainer libraryDir for shared… Pull request opened by aseetharam Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Summary Adds

apptainer.libraryDir

to the

purdue_gautschi

and

purdue_negishi

profiles so pipelines use RCAC's shared store of pre-pulled container images, and corrects two related points in the profile docs. Why Both profiles set only

apptainer.cacheDir

, pointing at per-user scratch. RCAC maintains a site-wide store of pre-pulled images, but nothing in either profile referenced it, so every user re-pulled and re-converted every image. This surfaced as a hard failure rather than just wasted time. A user running nf-core/sarek through our Open OnDemand gateway hit an OOM in the launcher job while converting two large GATK images to squashfs. Each conversion was killed partway, leaving a SIF with a valid header and no payload, and subsequent runs failed with:

FATAL: While checking container encryption: could not open image ...gatk4_gcnvkernel_htslib_samtools-c1e4292d6ee27439.img: ... not a valid squashfs image

Both images were already present and complete in the shared store, under exactly the filenames Nextflow generates. The failure was observed on Gautschi; Negishi had the same omission. Changes •

conf/purdue_gautschi.config

, `conf/purdue_negishi.config`: add `libraryDir`;

cacheDir

unchanged as the per-user fallback. •

docs/purdue_gautschi.md

, `docs/purdue_negishi.md`: document the shared store; replace

NXF_SINGULARITY_CACHEDIR

with

NXF_APPTAINER_CACHEDIR

, since these profiles enable the Apptainer scope and the Singularity variable is ignored. • Same docs:

module purge

to

module --force purge

in the prerequisites, since sticky modules otherwise inject a newer glibc that breaks containerised tools. Testing Tested on Gautschi with nf-core/sarek : with this change the previously re-pulled images resolve from the shared store and no download occurs.

libraryDir

requires Nextflow >= 22.12. nf-core/configs

#1177 Update pipeline configs Pull request opened by github-actions[bot] This is an automated PR to update pipeline configs for newly created nf-core pipelines. branch: 'update-pipeline-configs-34296202463' nf-core/configs

#1178 Add singularity libraryDir for shared containers (hazel.config) Pull request opened by sweavs111 --- name: Add singularity libraryDir for shared containers (hazel.config) about: This update to hazel.config adds the shared container library to be checked first (libraryDir) with a per-user fallback in a writable location if the contianer isn't found in the library (cacheDir). Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

scope in

.github/workflows/main.yml

• OPTIONAL: Add your custom profile path and GitHub user name to

.github/CODEOWNERS

(

**/<custom-profile>** @<github-username>

) nf-core/configs

#1179 Refactor Alphafold and Boltz configurations Pull request opened by SarahBeecroft Added AF3 functionality to the pipeline for Setonix and cleaned up some of the existing entries. Removed duplicate alphafold2_gcds entry and added alphafold3 parameters. Updated container options and cluster options for various processes. --- name: pawsey_setonix.config about: A new cluster config nf-core/configs

#1180 OIST: refresh profile (Slurm throttling, job arrays, sub-profiles) Pull request opened by charles-plessy Update of the existing

oist

profile. The settings that affect Slurm were reviewed and approved by the OIST cluster administrators (Scientific Computing and Data Analysis section, SCDA). Changes • Node constraint

-C epyc

(replaces

-C zen2

, no longer valid); time limit 96 h, the partition maximum. • Scheduler load: tasks submitted as job arrays of up to 96 (

process.array = 96

),

submitRateLimit = '12/1min'

,

queueSize = 208

,

queueStatInterval = '5 min'

,

pollInterval = '30 sec'

. • Sub-profiles, combined with `oist`: • `oist_short`:

short

partition on the Intel nodes. • `oist_saion`:

intel

partition of our second cluster. Adds

--requeue

and

exitReadTimeout = '1 day'

, because the partition preempts jobs and Nextflow's

--no-requeue

makes Slurm cancel them, which ends the run. • `oist_ci`: for test suites; no arrays, nf-core

test

resource limits, faster submission and polling. • Legacy

params.max_*

kept for pipelines older than nf-core/tools 3.0, and listed in

validation.ignoreParams

. • Documentation rewritten: Nextflow module choice,

-w

, Slurm settings, how to disable arrays (

-process.array 0

) for pipelines that are incompatible with them, sub-profiles. Testing •

nextflow lint

passes on 25.04.0, 25.10.4 and 26.04.6. •

nf-core/demo

on our cluster with

-profile oist,test

(job arrays) and

-profile oist,test,oist_ci

(single jobs), with Nextflow 25.10.4 and 26.04.6. --- • Your PR targets the

master

branch • You've included links to relevant issues, if any (none) Steps for adding a new config profile (update of an existing profile): • Add your custom config file to the

conf/

directory (

conf/oist.config

updated) • Add your documentation file to the

docs/

directory (

docs/oist.md

updated) • Add your custom profile to the

nfcore_custom.config

file in the top-level directory (already present) • Add your profile name to the

profile:

scope in

.github/workflows/main.yml

(already present) • OPTIONAL: Add your custom profile path and GitHub user name to

.github/CODEOWNERS

nf-core/configs

#1181 Sanger - fix withLabel to refer to correct GPU process label Pull request opened by prototaxites nf-core/configs

#1182 Switch fix-linting to the hardened nf-core/actions reusable workflow Pull request opened by mashehu This replaces the old fix-linting workflow (

.github/workflows/fix_linting.yml

, or

.github/workflows/fix-linting.yml

in pipelines created before nf-core/tools 3.3.0) with

.github/workflows/fix-linting.yml

, a short stub that calls the reusable fix-linting workflow from nf-core/actions (nf-core/tools#4485). The old workflow ran the pull request's own lint hooks in a job that also held the nf-core-bot token. The reusable workflow checks who asked for the fix, runs the pull request's code without any secrets, and pushes the result from a separate job that never runs pull request code. Commenting

@nf-core-bot fix linting

on a PR works as before. The next template sync makes the same change on

dev

. nf-core/configs

#1184 update paths for setonix Pull request opened by SarahBeecroft --- name: New Config about: A new cluster config Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

scope in

.github/workflows/main.yml

• OPTIONAL: Add your custom profile path and GitHub user name to

.github/CODEOWNERS

(

**/<custom-profile>** @<github-username>

) nf-core/configs

#1183 Document issue with running from home since it likely won't work on arrhenius Pull request opened by pontus EDIT: Changed to docs only Not sure if code to detect and flag likely problematic runs is overkill, especially since there's a false positive risk. I welcome opinions and would be happy to cut this to just documenting the issue. nf-core/configs

#1185 Bump minimum version to allow linting passing Pull request opened by jfy133 Currently we use 25.04 as our minimum version, however this doesn't work with the latest strict syntax, and we get some red-herring failings in CI tests. This bumps to a more up to date version of Nextflow that supports the strict syntax, and thus allow our configs CI tests to ✔️ nf-core/configs

#1161 Remove deprecated pipeline-specific specific Maestro config Pull request opened by jfy133 This is the last of the strict-syntax compliance campaign! Already communicated with the maintainers who are moving to a local copy. nf-core/configs

#1186 Update pipeline configs Pull request opened by github-actions[bot] This is an automated PR to update pipeline configs for newly created nf-core pipelines. branch: 'update-pipeline-configs-38329160401' nf-core/configs

#1188 fix(sanger): fix GPU profile so it works and tidy up linting issues Pull request opened by prototaxites • Fix the GPU config - merge

gpu

(non-template local label) and

process_gpu

into a single config block and fix the config inside. • Add

params.sanger_gpu_group

to allow configuration of LSF GPU group when needed. • Tidy and remove linter warnings from Nextflow nf-core/configs

#1189 changes in singularity settings Pull request opened by brovolia I see that a lot of people run into problems with the Singularity cache. Apparently, the original idea of using a shared cache under /work_ikmb/ikmb_repository/singularity_cache/ doesn't work. Each user still needs to write to the cache subdirectory, where access permissions are restricted. This seems to be causing a lot of issues. nf-core/configs

#1153 Fix apptainer access to node-local scratch Pull request opened by manascripts Apptainer containers currently only bind

/omics

. Minor change to bind

/local

globally in the profile so that LSF-provided local scratch remains accessible to all containerized tasks. nf-core/configs

#1132 [WIP] nf-co2footprint activation on CFC cluster Pull request opened by JosuaCarl on <!date^1781694987^{date_short}|2026-06-17T11:16:27Z> --- name: CFC nf-co2footprint activation about: Activation of the nf-co2footprint plugin per default Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any nf-core/configs

#1190 Update 1 flag and singularity module version in setonix config Pull request opened by SarahBeecroft This updates the singularity module version after the recent maintenance on Setonix, and removes an erroneous flag for alphafold3. I've also rebased my fork to nf-core master nf-core/configs

#1084 FIX: Strict syntax for eager/maestro Pull request opened by maxulysse --- name: New Config about: A new cluster config Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

scope in

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• OPTIONAL: Add your custom profile path and GitHub user name to

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**/<custom-profile>** @<github-username>

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#1082 FIX: Strict syntax for proteinfold/nci_gadi Pull request opened by maxulysse --- name: New Config about: A new cluster config Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

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scope in

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#1083 FIX: Strict syntax for eager/eva Pull request opened by maxulysse --- name: New Config about: A new cluster config Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

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#1081 FIX: Strict syntax for sarek/icr_davros Pull request opened by maxulysse --- name: New Config about: A new cluster config Please follow these steps before submitting your PR: • If your PR is a work in progress, include

[WIP]

in its title • Your PR targets the

master

branch • You've included links to relevant issues, if any Steps for adding a new config profile: • Add your custom config file to the

conf/

directory • Add your documentation file to the

docs/

directory • Add your custom profile to the

nfcore_custom.config

file in the top-level directory • Add your profile name to the

profile:

scope in

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**/<custom-profile>** @<github-username>

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