nf-core #help

Niklas Schandry

11/07/2025, 8:35 AM

If I put a profile into nf-core/configs, that defines more profiles, are those "inner" profiles available when I call the pipeline? I.e. can I do

nextflow run nf-core/pipeline -profile instution,sub_profile

where

sub_profile

is defined in

institution

Thomas Adams

11/07/2025, 10:43 AM

Hey all, I'm having reports from some users where a local config file at ~/.nextflow/config seems to be taking precedence over our institution profile on the nf-core repo passed with the

-profile

flag. Specifically, the profile passed uses singularity and not conda, but their local config does, and their run now looks to be using conda despite all the logs suggesting it read the profile correctly. I expect it's that I've missed something in the docs and need to update guidance internally, but I can't figure out how to have the specified profile override a local config. Thanks!

James Fellows Yates

11/07/2025, 12:55 PM

Does anyone have any suggestions to on how to track down the cause of a ConcurrentModificationException error within a process?

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ERROR ~ Error executing process > 'NFCORE_CREATETAXDB:CREATETAXDB:PREPROCESSING:FIND_CONCATENATE_DNA (1)'

Caused by:
  java.util.ConcurrentModificationException

ohno2 1

James Fellows Yates

11/07/2025, 12:59 PM

OK correction it's happening in multiple processes 😕

Evangelos Karatzas

11/10/2025, 10:49 AM

what happened to the draw.io paths library:

<https://github.com/nf-core/website/raw/main/public/images/graphic_design_assets/workflow_schematics_components/generic/nf-core_components.xml>

This doesnt work anymore

James Fellows Yates

11/12/2025, 10:28 AM

I have a feeling that I'm going insane... but before I confirm this - does anyone have any examples where they pass parameters to an internal string via a pipeline level parameter? e.g.

--tool_options "-k 2 -n 10"

This sort of thing?

Julio Diaz Caballero

11/13/2025, 4:25 PM

Hi all! I’m running some local tests and encountered a problem with a container that’s only available locally. In my module, I’ve set

container "assessassembly:latest"

, but Nextflow attempts to fetch it from quay.io. Does anyone know if there’s a way to explicitly indicate in the container line that the image should be used from the local environment rather than pulled from a registry?

Thiseas C. Lamnidis

11/14/2025, 9:59 AM

Hi everyone! I am having trouble merging the latest template (3.4.1) into nf-core/eager:dev : https://github.com/nf-core/eager/pull/1161 The default test profile is consistently failing because the runner runs into a java error:

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java.lang.IllegalArgumentException: The specified path does not exist: /home/runner/_work/eager/eager/~/tests/8bde3c40186e73112a6953d541d956b7/output/genotyping

That looks to me like a problem with the publishDir directive (since that is (part of) the publishDir of the process). BUT, I do not run into this problem at all locally, and cannot reproduce it outside of the GitHub runner. More info within thread

Evangelos Karatzas

11/14/2025, 10:07 AM

I am almost there with creating a downstream samplesheet with the new workflow output syntax, but struggling in the last bit. It's a very simple samplesheet with two columns:

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proteinfold_samplesheet = NFCORE_PROTEINFAMILIES.out.family_reps
        .map { meta, file ->
            [
                id: meta.id,
                fasta: file
            ]
        }

    publish:
    proteinfold_samplesheet = proteinfold_samplesheet

This is my current output directive:

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output {
    proteinfold_samplesheet {
        path { sample -> "proteinfold/${sample.id}/" }
        mode params.publish_dir_mode
        enabled !params.skip_proteinfold_samplesheet
        index {
            path 'proteinfold/samplesheet.csv'
            header true
            sep ','
        }
    }
}

It works fine but: 1. Can I also use sample.id somehow in the index? It keeps giving me errors whatever I tried. Otherwise two different runs will overwrite each other. 2. Can I turn off quoting in the index file that is created? currently it is like this:

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"id","fasta"
"mgnifams_test","/path/to/results/proteinfold/mgnifams_test/mgnifams_test_reps.faa"

Evangelos Karatzas

11/14/2025, 10:07 AM

@Thiseas C. Lamnidis sorry for the long message that might have covered your question 😛

😭 1

Jordi

11/17/2025, 10:50 AM

Hi all! From our site it seems that nf-core is down. Is there a way to check the service status? Maybe an announcement that I've missed? Thank you in advance.

Hovakim Grabski

11/17/2025, 12:53 PM

Hi Guys, #suggestion it is also possible to support Discord notification, by doing this:

def json_path = (

hook_url.contains("<http://hooks.slack.com|hooks.slack.com>") ||

(hook_url ==~ /https:\/\/discord\.com\/api\/webhooks\/\d+\/[A-Za-z0-9_\-]+\/slack/)

) ? "slackreport.json" : "adaptivecard.json"

Travis Dirks

11/17/2025, 8:49 PM

Nextflow AWS Batch + S3: Container Override for File Staging Is it possible to get methylseq working with AWSbatch sans fusion? Environment: • Nextflow: 25.04.8 • Pipeline: nf-core/methylseq v4.1.0 • Executor: AWS Batch • Work directory: S3 (s3://bucket/work/) Problem: Jobs fail with exit code 127 (AWS CLI not found). AWS Batch jobs use amazonlinux:2023 container for file staging, which lacks AWS CLI. Our custom ECR containers have AWS CLI installed, but aren't being used for staging operations. What We've Tried: 1. ❌ Removed cliPath from config (still fails) 2. ❌ Built custom containers with AWS CLI in private ECR 3. ❌ Used withName directives to override containers (only affects process execution, not staging) 4. ❌ Added jobDefinitionTemplate to config (ignored) Current Config:

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process {
    executor = 'awsbatch'
    queue = 'emseq-analysis'
    
    withName: 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQC' {
        container = '<http://ACCOUNT.dkr.ecr.us-east-1.amazonaws.com/fastqc-awscli:0.12.1|ACCOUNT.dkr.ecr.us-east-1.amazonaws.com/fastqc-awscli:0.12.1>'
    }
}

aws.batch {
    jobRole = 'arn:aws:iam::ACCOUNT:role/batch-job-role'
    executionRole = 'arn:aws:iam::ACCOUNT:role/batch-execution-role'
    volumes = '/tmp'
}

Question: How do we configure Nextflow AWS Batch to use our custom container (with AWS CLI) for S3 file staging operations? We cannot use Wave/Fusion due to licensing concerns for commercial use. Infrastructure works (jobs launch, IAM correct, 6000 vCPU quota approved), just need staging container fix. Expected: Our ECR containers used for ALL operations Actual: amazonlinux:2023 used for staging, fails before reaching our containers

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Is there a config parameter we're missing, or does AWS Batch + S3 work directory require Wave/Fusion?

Claudia Carter

11/18/2025, 2:03 PM

Not 100% sure where to ask but the link to the nf core draw.io cheatsheet which I find super useful for workflow diagrams has broken on the website - the PDF version is available but it would be great to get the draw io file back if possible 🙏 https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#components-cheatsheets

quick look 1

Anne Marie Noronha

11/18/2025, 9:24 PM

hi all! we're getting a weird error:

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N E X T F L O W   ~  version 24.10.4

ERROR ~ Unable to parse config file: '/data1/donoghum/pintoa1/FORTE/nextflow.config'

  Cannot read config file include: <https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config>


 -- Check 'logs/20251118_349_fusion_filtering' file for details

when i visit the url, i see the message:

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404: Not Found

when i try a slightly different url (https://raw.githubusercontent.com/nf-core/configs/refs/heads/master/nfcore_custom.config):

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429: Too Many Requests
For more on scraping GitHub and how it may affect your rights, please review our Terms of Service (<https://docs.github.com/en/site-policy/github-terms/github-terms-of-service>).

not sure what's happening. my latest pipeline version is 3.2.0

Scott Tbr

11/20/2025, 7:46 PM

Greetings everyone. Is there any way to suppress the formatting and color codes that are being added to the logs? It's making it very difficult to read anything. Is there a global setting that is needed, or a parameter to pass along to nextflow? I tried to use

-Dfile.encoding=ASCII

but that didn't help and may have even causes a failure with a groovy

java.nio.charset.UnmappableCharacterException

. Thanks for all of your help and suggestions!

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-[2m----------------------------------------------------[0m-
                                        [0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m        ___     __   __   __   ___     [0;32m/,-._.--~'[0m
[0;34m  |\ | |__  __ /  ` /  \ |__) |__         [0;33m}  {[0m
[0;34m  | \| |       \__, \__/ |  \ |___     [0;32m\`-._,-`-,[0m
                                        [0;32m`._,._,'[0m
[0;35m  nf-core/rnafusion v3.0.2-g42eb8d6[0m
-[2m----------------------------------------------------[0m-
[1mCore Nextflow options[0m
  [0;34mrevision                          : [0;32m3.0.2[0m
  [0;34mrunName                           : [0;32mirreverent_hoover[0m
  [0;34mcontainerEngine                   : [0;32msingularity[0m

Mathias Høj Jensen

11/21/2025, 3:04 PM

Hello everyone! 🙂 While checking the results of my RNA-seq pipeline output, I noticed that the

salmon/tx2gene.tsv

file contains multiple entries for the same gene symbol with suffixes like

_1

_2

, etc. Do you know what causes these

_1

_2

_3

, etc. suffixes, and how I can avoid this in future runs or handle it correctly downstream? For example: NM_001623.5 AIF1 AIF1 NM_001318970.2 AIF1 AIF1 XM_005248870.5 AIF1 AIF1 NM_032955.3 AIF1 AIF1 NM_001623.5_1 AIF1_1 AIF1_1 NM_001318970.2_1 AIF1_1 AIF1_1 XM_054329747.1 AIF1_1 AIF1_1 NM_032955.3_1 AIF1_1 AIF1_1 NM_001623.5_2 AIF1_2 AIF1_2 NM_001318970.2_2 AIF1_2 AIF1_2 XM_054330239.1 AIF1_2 AIF1_2 NM_032955.3_2 AIF1_2 AIF1_2 NM_001623.5_3 AIF1_3 AIF1_3 NM_001318970.2_3 AIF1_3 AIF1_3 XM_054330782.1 AIF1_3 AIF1_3 NM_032955.3_3 AIF1_3 AIF1_3 NM_001623.5_4 AIF1_4 AIF1_4 NM_001318970.2_4 AIF1_4 AIF1_4 XM_054331018.1 AIF1_4 AIF1_4 NM_032955.3_4 AIF1_4 AIF1_4 NM_001623.5_5 AIF1_5 AIF1_5 NM_001318970.2_5 AIF1_5 AIF1_5 XM_054331284.1 AIF1_5 AIF1_5 NM_032955.3_5 AIF1_5 AIF1_5

Kai Horny

11/24/2025, 10:43 AM

I need help with an nf-core download error. I run the nf-core download command with pulling of singularity images of a pipeline created freshly from the nf-core template and get the following error message:

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ERROR    Running 'nextflow inspect' failed with the following error                                                                                                             
ERROR    Command 'nextflow inspect -format json -profile singularity,test,test_full                                                                                             
         core-unit-bioinformatics-workflow-nxf-grzpreparation_main/main/main.nf' returned non-zero error code '1':                      
         > Unknown configuration profile: 'test'

I do not have configured anything with the test profile and do not intend to use it in this case. How to solve this error?

lilin

11/28/2025, 4:50 AM

A quick question: for Docker images that contain multiple tools (e.g., community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5), is there a quick way to find out the version of each tool? Does anyone know? Thanks!

Susanne Jodoin

11/28/2025, 2:12 PM

Hi, is there a best-practices way to allow PRs from a fork to an upstream nf-core pipeline to use the pipeline's secrets for running nf-test?

Elisabet Figuerola

11/28/2025, 2:51 PM

Hello everyone! We are performing targeted human DNA sequencing and want to check if there is any source of contamination from other species. Thus, we would need a strategy to efficiently identify non-human reads that we can use then in our pipeline to filter those reads. We ideally would like to start from BAM files (due to prior filtering). We would only need a simple human vs. non-human classification of the reads, not full taxonomic profiling. I've looked at some nf-core pipelines and seems taxprofiler and hgtseq could be the most convenient. However taxprofiler, apart from being a huge pipeline where we don't really need to know the full taxonomy of the reads, it starts with fastq files. On the other hand, hgtseq seem it is more focused on identifying integration sites of the non-host reads. Has anyone experienced this problem before or know of an efficient way to identify non-human reads directly (ideally) from a BAM file without requiring deep taxonomic analysis? Or if anyone knows any subworkflow or module that we could use? Thanks for any help!

lilin

11/30/2025, 3:40 PM

Hi there! I failed to build a Docker ARM64 container for STAR (v2.7.9a) using Seqera Containers. I tried several different STAR versions, and only v2.7.11b built successfully. However, I specifically need version 2.7.9a. How can I get Seqera Containers to build a Docker image for STAR v2.7.9a?

Nathalia Portilla

12/03/2025, 2:17 AM

Hello guys! I am a nextflow begginer learner, I want to know how to start building a new nexflow pipeline that can run local, HPC and eventually on nf-core. I have doubt about what structure follow. I really appreciate your advice.

Matthias De Smet

12/03/2025, 11:32 AM

I’m looking into using

rclone

for data staging. The manual says “it must be available in the task environment”. Does that mean the VM or the container?

Solenne Correard

12/04/2025, 9:56 AM

Hi! Samplesheet issues here 🙂 1. Is there good documentation on how to build and parse a samplesheet for a custom pipeline? We couldn't find it. 2. Here is a sample from my samplesheet

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sample,gff,fasta
Pb3A,Pb3A_genomic.gff,Pb3A_genomic.fna
PbeH,PbeH_genomic.gff,PbeH_genomic.fna

and here what we would like to do : run GFFread for each sample, knowing that it as to take the gff and fasta from the same row in the sheet (and do it for each row).

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GFFREAD (gff,fasta)

If someone could suggest the appropriate code, that would be great Thanks!

Carlos Villamizar

12/05/2025, 10:06 AM

Hello guys!! I am a begginer in the nextflow universe. I was wondering if anyone has tried the chipseq (chipseq: Introduction) pipeline for cell-free ChIP-seq (cfChIP-seq) analysis. Is it even possible?

#️⃣ 1

Venkat Malladi

12/08/2025, 5:08 PM

Is there a tool that can automatically make the subway diagrams from dag?

SimoneZaghen

12/09/2025, 9:42 AM

Hi! I am trying to run the test dataset to see if the rnaseq pipeline works. However, I get this error message. Any hint on how to solve this? Thank you

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-[nf-core/rnaseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (1)'

Caused by:
  Failed to pull singularity image
    command: singularity pull  --name depot.galaxyproject.org-singularity-fastqc-0.12.1--hdfd78af_0.img.pulling.1765270673200 <https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0> > /dev/null
    status : 143
    hint   : Try and increase singularity.pullTimeout in the config (current is "20m")
    message:
      INFO:    Downloading network image

Hanna Nordin

12/09/2025, 10:35 AM

Persistent Quota Limit Error (
AssocGrpCPURunMinutesLimit
) on DADA2_TAXONOMY (SLURM/PDC Dardel) Hi everyone, I'm running the nf-core/ampliseq pipeline (

v2.15.0

) on a SLURM-based cluster (Dardel/PDC) using the

singularity

profile. I'm experiencing a critical and persistent issue where all lightweight steps complete successfully, but the heavy process NFCORE_AMPLISEQ:DADA2_TAXONOMY_WF:DADA2_TAXONOMY
fails to start. The job is immediately stuck in PD (Pending) with the reason: (AssocGrpCPURunMinutesLimit)
. This indicates a quota/core-hour limit issue. My situation is slightly complex as my working directory is under project

naiss2025-22-1652

, but my core-hour quota is assigned to project

naiss2025-22-1066

now because I ran out of core-hours in the first project

naiss2025-22-1652

. The main problem is that the DADA2_TAXONOMY sub-job refuses to inherit the correct account (1066). Troubleshooting steps already attempted: 1. Setting
#SBATCH -A naiss2025-22-1066
in the wrapper script for the main Nextflow job. 2. Explicitly forcing the account in `nextflow.config`:

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process {
    clusterOptions = '--account=naiss2025-22-1066 --time=48:00:00'
}

3. Forcing the account via environment variable (intended to override all defaults):

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export NXF_CLUSTER_OPTS="--account=naiss2025-22-1066 --time=48:00:00"

The failure persists even with step #3. It appears this specific process is hardcoded or has a default resource request that always gets submitted without the correct

--account

flag to SLURM. Has anyone else encountered a persistent

AssocGrpCPURunMinutesLimit

error with the

DADA2_TAXONOMY

process on a SLURM system, even after trying NXF_CLUSTER_OPTS
? Are there any known workarounds within the nf-core configuration to specifically force the account for this module? Thanks for any advice!

Diego García

12/10/2025, 11:35 AM

Good morning! I work as an IT specialist at a research center in Spain. Some of our researchers have reported problems connecting to the web, and after running some tests, it seems that the web is blocking or not responding to our requests. Who can I contact to look into this?