Hello, I hope you are doing well. I would like to ask for your feedback on the approach I used to compare transcriptional responses between strains. For each stress condition, I identified differentially expressed genes and examined the pairwise overlap of up-regulated and down-regulated genes between two strains at a time, while excluding genes that were also regulated in the third strain under the same condition. To determine whether the observed overlaps reflected coordinated regulation rather than coincidence, I calculated the odds ratio and the corresponding Fisher’s exact test p-value for each pairwise comparison. This analysis was focused only on the number of shared versus strain-specific DEGs, without considering functional pathways or enrichment analysis at this stage. I would like to confirm whether this approach is appropriate for assessing similarity and divergence in transcriptional responses based purely on DEG overlap counts? Thank you

Hi all! I haven't foud yet similar topics, so in the meantime I'll drop a request for help here: I'm trying to update modules in a pipeline, I had no issues with the first two but then I'm only gettinr an error that I think is related to a python version. I can't paste the whole output but I have it, if needed I have latest versione of nextflow and nf-core/tools. And I have Python 3.13 ... please send help

(new-dev) nadiunix@LAPTOP-FAG8G0FQ:~/sammyseq$ nf-core modules update untar
...
TypeError: unhashable type: 'dict'

Question.. my pipeline stopped midway because I ran out of storage. Is there a way to resume from where the pipeline stopped? executor > local (393) [- ] NFC…DEX_BISMARK_BWAMETH:GUNZIP - [7c/6feebd] NFC…ex/reference_genome.fasta) | 1 of 1 ✔️ [f9/d43039] NFC…AT_FASTQ (SYNSC-741point2) | 57 of 57 ✔️ [81/777e70] NFC…Q:FASTQC (SYNSC-738point2) | 57 of 57 ✔️ [7a/0f6c02] NFC…IMGALORE (SYNSC-741point2) | 57 of 57 ✔️ [aa/bdf0cd] NFC…RK_ALIGN (SYNSC-741point2) | 57 of 57 ✔️ [0c/de53d8] NFC…UPLICATE (SYNSC-737point4) | 56 of 57 [f2/23fc15] NFC…OLS_SORT (SYNSC-730point4) | 37 of 56 [63/514907] NFC…LS_INDEX (SYNSC-742point1) | 36 of 37 [4a/82f621] NFC…XTRACTOR (SYNSC-742point4) | 10 of 56 [11/3977b9] NFC…CYTOSINE (SYNSC-742point4) | 8 of 10 [b8/7580fa] NFC…K_REPORT (SYNSC-739point2) | 9 of 10 [- ] NFC…UP_BISMARK:BISMARK_SUMMARY - [- ] NFC…QMETHYLSEQQUALIMAP_BAMQC | 0 of 37 [- ] NFC…ETHYLSEQMETHYLSEQMULTIQC -

The Nextflow syntax/language server is complaining about calling

meta

in prefix and args etc... in our

modules.config

Any suggestions how else to use these variables within in the

modules.config

file 'properly'?

Ah no wait I just need to wrap the whole thing in a closure, ingnore me

Hi everyone! I'm trying to run scRNA-seq on a dataset processed with inDropsv2, and have set up everything as directed by the documentation at nf-core. However, when I try to run the pipeline, I"m getting the following error: WARN: Failed to render execution report -- see the log file for details WARN: Failed to render execution timeline -- see the log file for details ERROR ~ Access Denied (Service: S3, Status Code: 403, Request ID: 79QGY0A2V62NX5WJ, Extended Request ID: XlL+AoLMLEjJYbG2oOP8gphZ+fC8ULP+TigvxjqokXMU5ZJmpZ4kVA0XJeuTijMZryP7bFaq9j49jQ2sN+cKlA==) (SDK Attempt Count: 1) -- Check script 'assets/nf-core/scrnaseq/subworkflows/nf-core/utils_nextflow_pipeline/main.nf' at line: 80 or see '.nextflow.log' file for more details Given the error, I'm fairly sure the error is due to an inability of the process to access my s3. I'm positive I've copied my aws access keys correctly into the mmc.config file, as I'm running the pipeline on a persistent headnode through MemVerge. I'm still relatively new to nextflow, and this is my first time running an nf-core pipeline, so it's entirely possible I'm missing something basic, but any help would be appreciated!

Hi there, I'm running the

circRNA

pipeline using 16 core and 320 gigs of RAM, everything was running fine until I reached the process `Process `NFCORE_CIRCRNACIRCRNABSJ_DETECTION:COMBINE_SAMPLES (all)`` terminated with error exit status (137):

Command executed [/home/z5628486/.nextflow/assets/nf-core/circrna/modules/local/combinebeds/filter/templates/filter.py]:
Command exit status:
  137

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  /opt/conda/lib/python3.12/site-packages/upsetplot/data.py:303: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`
    df.fillna(False, inplace=True)
  .command.run: line 168:    34 Killed                  /usr/bin/env python .command.sh
Container:
  /srv/scratch/work/singularity/community.wave.seqera.io-library-pandas_polars_pyarrow_upsetplot-8840b96e156438fc.img

it uses the whole 320gb of RAM; I tried putting limiter in the resourcelimits.config such as:

process {
    resourceLimits = [
        cpus: 16,
        memory: '300.GB',
        time: '23.h'
    ]
}

but the process ignores the config file and as such gets OOM killed again. Any suggestion would be helpful, thanks!

Hi! I'm about to create a new release for nf-core/pixelator, but GitHub says no, any idea what I'm doing wrong?

Hi all - is it possible to provide args for a given process at the workflow level? i.e. workflow level injection to overwrite module level

def args = task.ext.args ?: ''

for example, something similar to:

include { RASUSA as LONG_RASUSA  } from '../../../modules/nf-core/rasusa'

workflow DOWNSAMPLING {

    take:
    long_reads_ch // channel: [ val(meta), long_reads ]

    main:

    LONG_RASUSA (
            long_reads_ch,
            100,
            args: "--seed 1"
        )

or

include { RASUSA as LONG_RASUSA  } from '../../../modules/nf-core/rasusa'

def long_rasusa.ext.args = "--seed 1"

workflow DOWNSAMPLING {

    take:
    long_reads_ch // channel: [ val(meta), long_reads ]

    main:

    LONG_RASUSA (
            long_reads_ch,
            100
        )

I want to avoid using

conf/modules.config

or modifying/patching the underlying module

This message was deleted.

ERROR ~ Error executing process > 'NFCORE_CUTANDRUNCUTANDRUNPREPARE_GENOME:GUNZIP_GTF' Caused by: Failed to pull singularity image command: singularity pull --name depot.galaxyproject.org-singularity-ubuntu-20.04.img.pulling.1762379086803 https://depot.galaxyproject.org/singularity/ubuntu:20.04 > /dev/null status : 255 message: ERROR: pull is only supported for shub URIs i keep getting this error, does anybody know what the issue could be? Also fyi - i an running this on HPC which doesnt have docker installed so i had to create a conda environment and install singularity. However i keep getting this issue.

Hi all I am using nf-core proteinfold , I setting use_gpu=true but get error in multiqc step, in case I would like avoid to use gpu in multiqc step how can i do ?

Hello, I'm running nextflow run nf-core/rnadnavar -r 1.3.1 but it shows "Cannot find revision 1.3.1 --Make sure that it exists in the remote repository https:... . I want to run variant calling from rna-seq, anyone pls help.

Hi all - I try to run nf-core/hlatyping:

Hi all - I try to use the pipeline nf-core/hlatyping on a computer with 4 CPUs and 64GB RAM. The bam file is 65 GB big and aligns 150 nucleotides reads paired-end. I got as full message error:

Error executing process > 'NFCORE_HLATYPING:HLATYPING:CHECK_PAIRED (BAPA1)'

Caused by:
  Process `NFCORE_HLATYPING:HLATYPING:CHECK_PAIRED (BAPA1)` terminated with an error exit status (127)


Command executed:

  if [ $({ samtools view -H pbmc-1_OE0224_BEHINDMS_BAPA1_merged.mdup.bam -@2 ; samtools view pbmc-1_OE0224_BEHINDMS_BAPA1_merged.mdup.bam -@2 | head -n1000; } | samtools view -c -f 1  -@2 ) -gt 0 ]; then
      echo false > is_singleend.txt
  else
      echo true > is_singleend.txt
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HLATYPING:HLATYPING:CHECK_PAIRED":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  127

Command output:
  (empty)

Command error:
  .command.run: line 306: docker: command not found

Work dir:
  /Users/remy/work/38/04a4e23976be5292d1b39e7fb7c8e6

Container:
  <http://quay.io/biocontainers/samtools:1.16.1--h6899075_0|quay.io/biocontainers/samtools:1.16.1--h6899075_0>

Do you have an idea what is going wrong?

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

?

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!

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

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

Caused by:
  java.util.ConcurrentModificationException

OK correction it's happening in multiple processes 😕

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

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?

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?

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:

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

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:

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:

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:

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

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

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.

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"

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:

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

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

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

hi all! we're getting a weird error:

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:

404: Not Found

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

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