nf-core #help

phuaxmb

06/07/2025, 2:11 PM

Running into an issue with ERROR ~ .nextflow/history.lock (Permission denied) when trying to take over (using the resume flag) the running of a pipeline from someone else. I'm afraid changing the file permissions will cause the pipeline to restart completely, anyone knows or can advice on how I can properly resume the pipeline someone else had started?

Anastasios Bampalis

06/08/2025, 10:01 PM

Hello, I am new to Nextflow and nf-core, and I am trying to run the rnaseq pipeline. I have successfully installed Nextflow and tried running a test job to see if the pipeline is running properly, but I am getting the following error that persists even if I try to resume the pipeline: The exit status of the task that caused the workflow execution to fail was:

. The full error message was:

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Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fa)'

Caused by:
  Process `NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fa)` terminated with an error exit status (255)


Command executed:

  filter_gtf.py \
      --gtf genes.gtf \
      --fasta genome.fa \
      --prefix genome
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  [33mWARNING:[0m Could not lookup the current user's information: user: lookup userid 37544: no such process
  [31mFATAL:  [0m Couldn't determine user account information: user: lookup userid 37544: no such process

Work dir:
  /gpfs/scratch/hzq20zdu/nf_core/output_test/work/25/b87166cc5147c067fa8b22d32b8b94

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

I could not find any information through Google on errors regarding "userid information", so I thought to ask here for help. Any pointers or tips you can give me are welcome. I really appreciate any help you can provide.

Asher Preska Steinberg

06/09/2025, 2:01 PM

Hi all -- we've been encountering an error with some of our nextflow pipelines (both nf-core and ones we are developing) in which we are getting an error that seems to suggest that one of the jobs failed and was terminated by our hpc job scheduler (we're on a slurm-based HPC), yet when we go into the work directory it appears to have run successfully (outputs are in the work directory and exit code is 0). I’ve included a snippet of the error message in the comment. We see some discussion of this here: https://github.com/nextflow-io/nextflow/issues/2847 I'd also like to note that we take a look at the execution trace according to slurm the job completed successfully and there is a

.exitcode

file yet it seems the exit code status is marked null in the execution trace (this is attached as well). If anyone has suggestions it would be much appreciated.

Derrik Gratz

06/09/2025, 4:05 PM

Is there a way to use secrets in

nf-test

? I'm writing a module for software that requires a license file (which are free for academic use) and I'd like to write tests that can run without sharing my personal license

Gaspard Ichas

06/10/2025, 7:33 AM

Hi everybody, @Louis Le Nézet and I wonder how to integrate a tool with a non-commercial license into nf-core. I'm working on the phaseimpute pipeline and would like to include Impute5, but the developers from Oxford University Innovation have informed us that they cannot authorize packaging in Bioconda as the software is under a restricted licensing model (likely non-commercial use only). We would like to know if you had an idea to bypass this constraint. If not, we thought to ask users to download manually the binary. Thanks for your guidance!

suzannejin

06/10/2025, 4:36 PM

anybody know how this code:

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ch_results
        .combine(inputs.filter_params, by:0)
        .view()

produces empty channel (fail to match) even though this code will not:

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ch_results
        .combine(inputs.filter_params)
        .map { meta1, file, meta2, filter_params ->
            if (meta1 == meta2) {
                return [meta2, file, filter_params]
            }
        }
        .view()

Xinpeng Zhang

06/11/2025, 2:00 AM

Hi all, I have a question about the input sample sheet format (for example, the default data sheet included meta, fastq1, fastq2). It seems like there’s not a common way to change the format. Some pipelines may change it in the “utils_nfcore_xxxx_pipeline/main.nf, and some may do it in the workflow/main.nf. I checked the docs, and it didn’t mention anything about it. Could you please give me some suggestions, or should we have a common format and location (for example, at the workflow/main.nf)to define it?

👀 1

Eric Salazar

06/11/2025, 4:15 AM

I am trying to currently run a pipeline however I keep getting an error message that says ERROR ~ Cannot invoke method contains() on null object? I am trying to run pgs_calc from PGS calculator to get a risk score. I am using a VCF file and scoring file

John Michael Egana

06/11/2025, 4:54 AM

I am trying to override a process command using

ext.args

to append additional flags. This is useful when tweaking a process that are not programmed as a

params

value. By adding process-specific

ext.args

in a config file, you have a flexibility to do so. Question is, can you also override the process

output

directive in the config file without changing the source code (i am using an nf-core pipeline)? My goal here is to make an output be optional since I tweaked the command that resulted in a file not being outputted.

Layton

06/11/2025, 3:59 PM

Hello, I'm having a frustrating error with nf-core/Metaboigniter that I was hoping someone could help me with, the adduct decharger step seems to consistently fail in negative mode and I can't find a reason why or solution for it. The error seems to be related to an inability to establish a "default" adduct despite the fact i have my probabilities set with M-H as highest (default) probability.

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ERROR ~ Error executing process > 'NFCORE_METABOIGNITER:METABOIGNITER:ANNOTATION_REQ:OPENMS_METABOLITEADDUCTDECHARGER (42-r001)'

Caused by:
  Process `NFCORE_METABOIGNITER:METABOIGNITER:ANNOTATION_REQ:OPENMS_METABOLITEADDUCTDECHARGER (42-r001)` terminated with an error exit status (8)


Command executed:

  mkdir output
  
  MetaboliteAdductDecharger \
                      -in 42-r001.merged.featureXML -out_fm output/42-r001.featureXML -algorithm:MetaboliteFeatureDeconvolution:potential_adducts H-1:-1:0.6 CH3COO:-1:0.4 -algorithm:MetaboliteFeatureDeconvolution:charge_min 1 -algorithm:MetaboliteFeatureDeconvolution:charge_max 2 -algorithm:MetaboliteFeatureDeconvolution:charge_span_max 1 -algorithm:MetaboliteFeatureDeconvolution:q_try heuristic -algorithm:MetaboliteFeatureDeconvolution:retention_max_diff 2.5 -algorithm:MetaboliteFeatureDeconvolution:retention_max_diff_local 2.0 -algorithm:MetaboliteFeatureDeconvolution:mass_max_diff 10 -algorithm:MetaboliteFeatureDeconvolution:unit ppm -algorithm:MetaboliteFeatureDeconvolution:max_neutrals 1 -algorithm:MetaboliteFeatureDeconvolution:use_minority_bound true -algorithm:MetaboliteFeatureDeconvolution:max_minority_bound 1 -algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap 0.66 -algorithm:MetaboliteFeatureDeconvolution:intensity_filter -algorithm:MetaboliteFeatureDeconvolution:negative_mode -algorithm:MetaboliteFeatureDeconvolution:default_map_label 'decharged features'
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METABOIGNITER:METABOIGNITER:ANNOTATION_REQ:OPENMS_METABOLITEADDUCTDECHARGER":
      openms: $(OpenMSInfo | awk '/OpenMS Version/{getline; getline; print $3}')
  END_VERSIONS

Command exit status:
  8

Command output:
  Parameters 'retention_max_diff' and 'retention_max_diff_local' are unequal, but no RT shift of adducts has been defined. Setting parameters to minimum of the two.
  MassExplainer table size: 2
  Generating Masses with threshold: -1.42712 ...
  done

Command error:
  Parameters 'retention_max_diff' and 'retention_max_diff_local' are unequal, but no RT shift of adducts has been defined. Setting parameters to minimum of the two.
  MassExplainer table size: 2
  Generating Masses with threshold: -1.42712 ...
  done
  Error: Unexpected internal error (WARNING!!! implicit number of default adduct is negative!!! left:-2 right: -2
  )

Work dir:
  /home/plashmore/projects/gitlab/naca-smoke-taint/03-metaboigniter/work/5b/4095405550b2dd572032ba76fd2a20

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Failed to invoke `workflow.onComplete` event handler

 -- Check script '/home/plashmore/.nextflow/assets/nf-core/metaboigniter/./workflows/../subworkflows/local/utils_nfcore_metaboigniter_pipeline/main.nf' at line: 123 or see '.nextflow.log' file for more details

#️⃣ 1

Jimmy Lail

06/12/2025, 5:27 PM

Hello, I am trying to learn about nextflow testing and how to write/incorporate stubs to test a local module. I was wondering what is the recommended documentation or tutorials for doing so? I found https://training.nextflow.io/latest/nf4_science/genomics/04_testing/#1-test-a-process-for-success-and-matching-outputs but was wondering if there are any other materials recommended? -Thanks!

Limin Chen

06/12/2025, 9:04 PM

Hi, I tried to create a channel from a list, here is my code:

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thread_ch = channel.of(params.threads)
    ref_ch = channel.fromPath(params.ref)
        .map { it.toString() }
    fq_ch = channel.fromPath(params.fq)
        .map { it.toString() }
    saw_ch = channel.fromPath(params.saw_path)
        .map { it.toString() }

    cleanreads_list = saw_ch.concat( id_ch, whitelist_ch.flatten(), fq_ch, ref_ch, thread_ch )
        .collect()
    //    .view()
    cleanreads_ch = Channel.fromList( cleanreads_list ).view()

However, it gave me error: N E X T F L O W ~ version 24.10.5 Launching

<http://STRS_mategenomics_1.nf|STRS_mategenomics_1.nf>

[stupefied_raman] DSL2 - revision: 9a36a8591d [- ] WHITELIST - Missing process or function Channel.fromList([DataflowVariable(value=null)]) I guest the

channel.fromList

ran before the list is created. Why did this happen and how to fix it? I care about the elements order as they are, that's why I use

concat

. Any suggestions are greatly appreciated.

Nathan Tear

06/16/2025, 3:13 AM

Hello, Sorry if this has already been asked. I am a little confused with setting of resource limits. 1. Is this only possible via a custom.config or can they be added to the nextflow.config file? I want to make the run command as simple as possible for users so attempting to avoid the use of an added -c tag. 2. Is it possible to have resources customisable using a params file? Many Thanks

yokofakun

06/16/2025, 11:49 AM

Hi all, I'm running a workflow using profile=conda, but for one specific process I need to use apptainer. Is there any way to specify this in the process ? (I tried

process XX { conda.enabled=false;... }

but but it didn't work ('executable not found' as if there was no container ).

Yuxin Ning

06/16/2025, 12:01 PM

Hi all, how should we manually generate new snapshots for

.github/snapshots/

yokofakun

06/16/2025, 12:17 PM

follow up of https://nfcore.slack.com/archives/CE6SDBX2A/p1750074746040609?thread_ts=1750074599.545959&cid=CE6SDBX2A what is the correct syntax to exclude a set of process by Name using the negate operator (

): if tried:

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withName: '!PROC1|PROC2|PROC3' {
        container = null
    }

and

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withName: '!(PROC1|PROC2|PROC3)' {
        container = null
    }

but that didn't work.

Yeahji

06/16/2025, 3:48 PM

Hello all Im trying to run nf-core/rnavar for variant calling for Apis mellifera and tried to build a customised database for it using --snpEff_db I am struggling with building the database They are failing to generate protein.fa and cds.fa even tho I am using gff file Did anyone have same problem or figure out to use any different way than using the customised one ? Thanks !!

Dave Jones

06/17/2025, 12:55 PM

Hello 👋 I'm trying to debug a new pipeline, but I'm encountering unexpected behaviour in the channels api. In a brand new project initialised with nf_core pipelines create, I'm running the following:

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<http://log.info|log.info> "About to run squares"
    nums = Channel.of(1, 2, 3, 4) 
    square = nums.map { it -> it * it } 
    square.view()
    <http://log.info|log.info> "Successfully ran squares"

Which is printing

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About to run squares
Successfully ran squares

to stdout. My question is, how do I access the output of the view method?

Sylvia Li

06/18/2025, 10:56 PM

Hi, I just made a new pipeline from nf-core pipelines create, but it already shows that I have errors in the nextflow.config/modules.config file. for example line279 nextflow.config

\033[0;35m  nf-core/bactiseq ${manifest.version}\033[0m

manifest is not defined or line 16 modules.config

path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },

Task is not defined i havent added any of my own code so i am not sure why it's saying it is an error? I am running on VScode version 1.100.3 with nextflow extension version 1.5.0 thanks i am not sure if this is something I set up wrong or what I should do. I did do a test run through

nf-core <pipelinename> -profile test,docker --outdir results

it did run fine, no errors or anything but not sure if these errors will cause more down the line?

Sylvia Li

06/18/2025, 10:57 PM

message has been deleted

Louis Le Nézet

06/19/2025, 8:09 AM

Hi, I have the following function that simply get the region from a fasta index:

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def getRegionFromFai(input_region, ch_fasta) {
    def ch_regions = Channel.empty()
    // ch_fasta.view()
    // Gather regions to use and create the meta map
    if (input_region ==~ '^(chr)?[0-9XYM]+$' || input_region == "all") {
        ch_regions = ch_fasta.map{ it -> it[2] }
            .splitCsv(header: ["chr", "size", "offset", "lidebase", "linewidth", "qualoffset"], sep: "\t")
            .map{it -> [chr:it.chr, region:"0-"+it.size]}
        if (input_region != "all") {
            ch_regions = ch_regions.filter{it.chr == input_region}
        }
        ch_regions = ch_regions
            .map{ [[chr: it.chr, region: it.chr + ":" + it.region], it.chr + ":" + it.region]}
    } else {
        if (input_region ==~ '^chr[0-9XYM]+:[0-9]+-[0-9]+$') {
            ch_regions = Channel.from([input_region])
                .map{ [[chr: it.split(":")[0], "region": it], it]}
        } else {
            error "Invalid input_region: ${input_region}"
        }
    }
    return ch_regions
}

~~However when I test it with nf-test if the ch_fasta.view() is commented out then the test fail with:~~ java.lang.IndexOutOfBoundsException: toIndex = 3
. What could be the reason ? ~~I'm leaning for a staging issue of the file.~~ However the

function.result

is empty.

Sachintha Wijegunasekara

06/21/2025, 2:24 AM

Hi. I am trying to limit the maximum resource usage in nfcore/funscan since mmseqs is attempting to run two samples simultaneously, which is causing to run out of memory. I have made the following config file.

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process {
  resourceLimits = [
    cpus: 48,
    memory: 450.GB,
    time: 120.h
  ]
}

Is the correct command to run wiht the config

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nextflow -bg -c maxresourceLimits.config run nf-core/funcscan my_command

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nextflow -bg -C maxresourceLimits.config run nf-core/funcscan my_command

Cheyenne

06/22/2025, 12:52 PM

Suppose I have checkpoint file for one of my modules, is there built in functionality to make sure it resumes from my checkpint or should I just add the checkpoint file as flag and then handle it from within the module

Dave Jones

06/23/2025, 10:07 AM

Hi. I'm having an issue with module installation. Unfortunately I had to interrupt the installation process, and when reattempting I now get an error:

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nf-core modules install gfatools/gfa2fa


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.3.1 - <https://nf-co.re>


ERROR    tuple index out of range

I'm not sure what I've broken. Is there some way to reset the relevant project state and proceed with an install?

Thad Edens

06/23/2025, 2:44 PM

How can I write a process/workflow that consumes a channel and makes the output of a task available to the next task? The use case is described here. The process/workflow launches a singularity container, runs a nextflow pipeline using slurm executor and outputs a singularity image of its workDir. The next task needs to mount that squashfs image to the containers file system.

Thad Edens

06/23/2025, 4:19 PM

I meant to write "...slurm executor and outputs a squashfs image ..." For some reason I am not able to edit that comment.

Pedro Mendez

06/23/2025, 8:41 PM

Hi there, I'm trying to run the nf-core/rnaseq pipeline on Ubuntu 22.04 with the following specs: see pic uploaded I installed locally the following dependencies, just in case: • nextflow • nf-core • fq • salmon • fastqc • umitools • cutadapt • trim_galore • samtools • bbmap • sortmerna • star • picard • stringtie • bedtools • ucsc-bedgraphtobigwig • dupradar • preseq • rseqc Then, I tried to run the following command to test the pipeline:

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nextflow run nf-core/rnaseq -profile test,conda --outdir rna_results_06_22v3

it returned the following error:

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[-        ] NFCORE_RNASEQ:RNASEQ:MULTIQC                                                               -
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/trimgalore/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-3cb1f98716d46bb0-7ee73282f0ad4cb3bfb895355fb91bd7]
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/fq/lint/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-930a3c51c1f4168e-16bfc74f50473b17f7bf05d44dde0205]
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/fastqc/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-44672b7451831d70-3ea42529974ca5a54ae5623eacfbc76a]
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/untar/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-6336a1b7bbcc0c23-cac18ad63488da9f5109ab1f794a29f6]
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnaseq] Pipeline completed with errors-
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/cat/fastq/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-dc4947c2aa26d50f-809d7bbc0708e58c59ba558c02e39e97]
WARN: Directive `process.shell` cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
]
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)'

Caused by:
  Process `NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)` terminated with an error exit status (126)


Command executed:

  # Not calling gunzip itself because it creates files
  # with the original group ownership rather than the
  # default one for that user / the work directory
  gzip \
      -cd \
       \
      gfp.fa.gz \
      > gfp.fa
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA":
      gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  .command.run: line 299: .command.run: Permission denied

Work dir:
  /home/pmendez00/nfcore_runs/work/34/d295729ecc2cd244e2683cc5195745

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

I tried running it with Docker as well and I get the same error. Also uploading the .nextflow.log file. Has anyone found the same error? THANKS FOR YOUR HELP!!

John Doe

06/23/2025, 11:16 PM

Hello, I’m new to bioinformatics and would appreciate some guidance on the general workflow for WGCNA analysis in disease studies. If there are any tutorials or resources you can point me to, that would be appreciated! I watched the tutorial from Bioinformagician, but she only performs WGCNA using count data. Expression data: What type of expression data is best for WGCNA? Should I use VST-transformed counts, TPMs, FPKMs, or something else if starting from FASTQ files? My plan is to first generate raw counts using nf-core/rnaseq, then apply VST transformation in DESeq2 before WGCNA. Is this okay? Sample inclusion: If I have both healthy controls and disease samples, should I include all samples or only disease samples? I’ve read that WGCNA doesn’t require controls, but I’ve also seen suggestions that a reference group can help. I’m planning to combine datasets. While controls are age- and sex-matched within each dataset, there's still variability—especially across datasets. Should I limit WGCNA to disease samples only and apply batch correction? Preprocessing pipeline: What’s the best pipeline/tool for local processing of FASTQ files for downstream WGCNA? I’m considering this pipeline: FastQC, fastp, HISAT2, featureCounts. Would you recommend this over using nf-core/rnaseq or GenPipes? Use of fastp: Even if no adapters are detected, would you still recommend using fastp for consistency across datasets? Thanks in advance!

ramya ranaganathan

06/24/2025, 2:30 PM

Hi all, I am trying to test the nf-core/chipseq -profile test and the pipeline is failing anyone recently used this pipeline successfully? I am attaching the nextflow log file and error report if anyone can help that would be great . Thanks Ramya

#️⃣ 1

Joris van Steenbrugge

06/25/2025, 6:51 AM

Hi all, I'm running into an interesting issue when running nf-core module rseqc/readdistribution. The error I get (sometimes, but not always) :

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.command.sh: line 9: sampleA.read_distribution.txt: cannot overwrite existing file

And the command executed is:

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read_distribution.py \
      -i sampleA.dedup.bam \
      -r GRCh38_gencode_v22_CTAT_lib_Mar012021.ref_annot.gtf.bed \
      > sampleA.read_distribution.txt

I assume this error is cause by the shell configuration (noclobber), but I cannot really explain why sampleA.read_distribution.txt would already be present in the working directory of that process, as the only inputs are the bam file and the bed file. sampleA.read_distribution.txt is only an output of the process. Has anyone experienced something similar before? Thanks!