hello everyone! Trying to run sarek with Manta and Strelka I got an permission error. May be someone know what could be the reason? A search for a same error in slack showed that is is not common and havenot been reported.. runWorkflow.py is executable itself

ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (D_vs_G)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC (D_vs_G)` terminated with an error exit status (1)


Command executed:

  configManta.py \
      --tumorBam SJBALL255_D.WholeGenome.bam \
      --normalBam SJBALL255_G.WholeGenome.bam \
      --reference Homo_sapiens_assembly38.fasta \
       \
      --runDir manta \
      --callRegions wgs_calling_regions_noseconds.hg38.bed.gz \
  
  
  python manta/runWorkflow.py -m local -j 15
  
  mv manta/results/variants/candidateSmallIndels.vcf.gz \
      D_vs_G.manta.candidate_small_indels.vcf.gz
  mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
      D_vs_G.manta.candidate_small_indels.vcf.gz.tbi
  mv manta/results/variants/candidateSV.vcf.gz \
      D_vs_G.manta.candidate_sv.vcf.gz
  mv manta/results/variants/candidateSV.vcf.gz.tbi \
      D_vs_G.manta.candidate_sv.vcf.gz.tbi
  mv manta/results/variants/diploidSV.vcf.gz \
      D_vs_G.manta.diploid_sv.vcf.gz
  mv manta/results/variants/diploidSV.vcf.gz.tbi \
      D_vs_G.manta.diploid_sv.vcf.gz.tbi
  mv manta/results/variants/somaticSV.vcf.gz \
      D_vs_G.manta.somatic_sv.vcf.gz
  mv manta/results/variants/somaticSV.vcf.gz.tbi \
      D_vs_G.manta.somatic_sv.vcf.gz.tbi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA:MANTA_SOMATIC":
      manta: $( configManta.py --version )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/usr/local/bin/configManta.py", line 182, in <module>
      main()
    File "/usr/local/bin/configManta.py", line 170, in main
      makeRunScript(workflowScriptPath,os.path.join(workflowDir,"mantaWorkflow.py"),"MantaWorkflow",primarySectionName,iniSections)
    File "/usr/local/share/manta-1.6.0-1/lib/python/makeRunScript.py", line 76, in makeRunScript
      os.chmod(scriptFile,0755)
  OSError: [Errno 1] Operation not permitted: 'manta/runWorkflow.py'

how to pass argument through

template

, I am trying to pass batch info and sample_info to a module but it is not working, the part where I am trying to pass info to the module (from workflow ) is given below,

ch_samplesheet
    .map { meta, _ -> tuple(meta.id, meta.sample_batch) }
    .set { ch_batch }


ch_derfinder = DERFINDER.out.Rda


  BATCHCORRECTION (
      ch_batch,
      ch_derfinder
                 )

and the module's main.nf is given below,

process BATCHCORRECTION {
    // tag "$meta.id"
    label 'process_single'

    conda "${moduleDir}/environment.yml"
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        '<oras://community.wave.seqera.io/library/bioconductor-sva:3.54.0--6dce402d4a7742a0>':
        'community.wave.seqera.io/library/bioconductor-sva:3.54.0--6ac32dfb26a67399' }"

    input:
    tuple val(sample_id), val(batch)
    tuple val(meta), path(derfinder_obj)

    output:
    tuple val(meta), path ("*.csv")  , emit: count_matrix
    path "versions.yml"           , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    template "batctcorrection_script.R  --id '\${sample_id}' \\
      --batch '\${batch}'"

}

but the way above I am getting error which says that template file not found, although the script batctcorrection_script.R is in the

templates

folder. Any leads where I am getting it wrong ?

I'm having trouble with my

FreeBayes

process as part of a larger read mapping subworkflow. For some reason the input channel for my bam/bai files wont include all samples even if all the bam files are being created by the previous process. I'm expecting there to be two FreeBayes tasks but only only one runs. If I resume the pipeline, the other one runs but never both. I can't see anything obvious and have tried a few different things but no success. The input channels for FreeBayes are being created as follows:

ch_freebayes_fasta = ch_fasta // channel: [ val(meta), path(reference), path(fai)]

.join( ch_faidx )

freebayes_input = ch_bam  // channel: [ val(meta), path(bam) ]

.join( ch_bam_index ) // channel: [ val(meta), path(bam), path(bam_index)]

.map{

meta, bam, bai -> [ meta, bam, bai, [], [], [] ]

}

BAM_VARIANT_CALLING_SORT_FREEBAYES_BCFTOOLS (freebayes_input,

ch_freebayes_fasta,

[ [:], [] ],

[ [:], [] ],

[ [:], [] ]

)

any idea on this lint error? https://github.com/nf-core/modules/actions/runs/14330785888/job/40166154247?pr=8229

Anybody has issue ever with docker container not being able to be pulled: https://nfcore.slack.com/archives/CHN5BV5DW/p1744215290988759

Hi ! I'm looking for an alignment file with HLA location in it to be use by the modules

HLALA_TYPING

. There is two files existing in the test datasets repository

example_hla_pe.bam

and

example_hla_pe.sorted.bam

but the reads are not properly paired and the module crash. Is there anywhere some file with HLA region or at least a bit of the chr6 ?

I am trying to benchmark a pipeline on multiple releases of a pipeline. When I use

-r

on older versions they're failing to find a

bin/script.py

that has since been deleted in the latest release. The stdout states the correct version of the pipeline but I can't think of a reason as to why it is failing to find the appropriate file. For context I am running this pipeline at the last three releases.

I am confused how to maintain the

TEMPLATE

branch in an nf-core repo, since there is almost always conflicts when the template is updated, and we have to resolve them... every... time... Should we be updating that branch to

dev

after each merge? I also see that it always tries to update sections in the README and other places that need to be filled in when first authoring a pipeline. Is there a way to ignore those sections?

anybody knows how to groupTuple by all the elements except last one? dynamically (varied size)?

Hello, I am trying to override the 'custom.config' in the nf-core/rnaseq, like below screenshot. However, my custom config file is not overridden in the log. the configFiles line was empty. is there any way to fix it? any help is appreciated.

Hello, Question about using nf-core modules: If I need to provide extra input into a function of nf-core module that doesnt allow that input channel, do I need to actually adjust the main.nf of the module itself? Since this cannot be an external argument Im not sure how I could do this in module.config. When I ask Seqera AI it also suggests to modify the main.nf of the nf-core module, which does not make sense for reproducibility.

Hello! is there an nf-core pipeline that does basic QC and multiQC for fastq sequences? Sometimes that is all that we need! I found https://nf-co.re/seqinspector/dev/ but it seems to still be under-development. Is this the main option?

How can you get the subfolder from an untarred output? I’m using the

nf-core/untar

module (https://github.com/nf-core/modules/tree/master/modules/nf-core/untar) and just want to access the

data

subdirectory output from the untarred file (see full file listing below). I tried

input[0] = [ file("$UNTAR.out.untar[1]/data"),  "5.73-104.0" ]

but that created this error:

(nf-core-v2)
 Tue 15 Apr - 14:19  ~/code/nf-core-proteinannotator   fork ☊ olgabot/add-interproscan ✔ 
  nf-test test modules/local/interproscan/setup/tests/main.nf.test --profile docker

zsh: correct 'test' to 'tests' [nyae]? n

🚀 nf-test 0.9.2
<https://www.nf-test.com>
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr


Test Process INTERPROSCAN_SETUP

  Test [1f1cc972] 'interproscan - setup' FAILED (0.006s)

  groovy.lang.MissingPropertyException: No such property: UNTAR for class: com.askimed.nf.test.lang.process.ProcessContext



FAILURE: Executed 1 tests in 0.01s (1 failed)

Here is the

main.nf.test

file I’m working on: https://github.com/nf-core/proteinannotator/pull/9/files#diff-4835d822ff0817fe330b3949d5e1ac3fb794b5cea545ab919f2c6bd7dde4175f

(nf-core-v2)
 Tue 15 Apr - 13:54  ~/code/nf-core-proteinannotator/modules/local/interproscan/setup/tests/fixtures   fork ☊ olgabot/add-interproscan 2☀ 5● 
  ll ~/Downloads/interproscan-5.73-104.0
Permissions User Group  Size       Date Modified       Git                  Name
drwxr-xr-x  olga staff  49 GB Tue Apr 15 12:59:52 2025 --    .
drwx------  olga staff 139 GB Tue Apr 15 13:34:51 2025 --    ..
.rw-r--r--  olga staff 6.0 KB Thu Apr  3 13:52:22 2025 --    .DS_Store
drwxr-xr-x  olga staff 100 MB Wed Jan 29 09:26:28 2025 --    bin
drwxr-xr-x  olga staff  48 GB Tue Apr  1 10:57:41 2025 --    data
.rwxr-xr-x  olga staff 362 KB Wed Jan 29 09:29:42 2025 --    interproscan-5.jar
.rw-r--r--  olga staff 208 KB Thu Mar 20 12:54:23 2025 --    interproscan-data-5.73-104.0.tar.gz
.rw-r--r--  olga staff 4.4 KB Wed Jan 29 09:26:29 2025 --    interproscan.properties
.rwxr-xr-x  olga staff 1.6 KB Wed Jan 29 09:26:14 2025 --    interproscan.sh
drwxr-xr-x  olga staff  76 MB Wed Jan 29 09:30:16 2025 --    lib
.rw-r--r--  olga staff 142 B  Wed Jan 29 09:26:33 2025 --    readme.txt
.rwxr-xr-x  olga staff 3.5 KB Thu Apr  3 14:03:24 2025 --    setup.py
drwxr-xr-x  olga staff 646 KB Wed Jan 29 09:26:33 2025 --  󱧼  src
drwxr-xr-x  olga staff 620 MB Tue Apr 15 10:43:45 2025 --    temp
.rw-r--r--  olga staff 4.0 KB Wed Jan 29 09:26:34 2025 --    test_all_appl.fasta
.rw-r--r--  olga staff  17 KB Tue Apr 15 10:43:45 2025 --    test_all_appl.fasta.tsv
.rw-r--r--  olga staff  61 KB Wed Jan 29 09:26:32 2025 --    test_convert_mode.xml
.rw-r--r--  olga staff 6.4 KB Wed Jan 29 09:26:33 2025 --    test_nt_redundant.fasta
.rw-r--r--  olga staff 5.3 KB Wed Jan 29 09:26:33 2025 --    test_nt_seqs.fasta
.rw-r--r--  olga staff 205 KB Wed Jan 29 09:26:32 2025 --    test_nt_seqs_convert_mode.xml
.rw-r--r--  olga staff 1.6 KB Wed Jan 29 09:26:33 2025 --    test_proteins.fasta
.rw-r--r--  olga staff  82 KB Wed Jan 29 09:26:33 2025 --    test_proteins_convert_mode.xml
.rw-r--r--  olga staff 1.6 KB Wed Jan 29 09:26:33 2025 --    test_proteins_new.fasta
.rw-r--r--  olga staff 4.2 KB Wed Jan 29 09:26:33 2025 --    test_proteins_redundant.fasta
.rw-r--r--  olga staff 272 B  Wed Jan 29 09:26:14 2025 --    test_single_protein.fasta
drwxr-xr-x  olga staff 134 MB Wed Jan 29 09:26:34 2025 --    work

Does anyone else has some Github server error ? https://github.com/nf-core/modules/pull/8147

Hello! I was looking for a general nf-core QC pipeline and I ran into seqinspector, it seems close to what I was looking for, which is just something that we can run on a set of fastq files to check their quality. Do you think this is the intention of the pipeline and that it is more or less ready to be used? I tried running it with this:

sample,fastq_1,fastq_2,rundir,tags
MS003,MS003_blood_S1_L001_R1_001.fastq.gz,MS003_blood_S1_L001_R2_001.fastq.gz,241206_GAR-0032_0066_3_3B0444T,paired_sample

But it complained: * -- Entry 1: Missing required value: lane Do the file names need to say "lane"??? I was also confused about the rundir. What if I don't have one?

Hi, i have something I tried to figure out for the whole afternoon 🤯 Your help is much appreciated!! I want to ask if it possible to convert a channel to string in the workflow. I read a bit and it seems to be not doable in DSL2. But i guess shall be a way around I have a workflow like below, apparently because

genome

is a input channel and

${genome}

did not work in

fasta       = Channel.fromPath("${params.reference_path}/${genome}/genome.fa"

. But any solutions? I also noticed

genome == "GRCh38"

actually works, makes sense?

workflow {

    take:
    genome      

    main:
    genome.view { println "Genome string is: genome: ${it}" }
     if( params.reference_path ) {
     fasta       = Channel.fromPath("${params.reference_path}/${genome}/genome.fa", checkIfExists: true).map { file -> tuple([ id: file.getSimpleName() ], file) }.collect()
}else{

        if(genome == "GRCh38"){
            fasta   = params.fasta ? Channel.fromPath(params.fasta, checkIfExists: true).map{ file -> tuple([id: file.getSimpleName()], file) }.collect()
                                : Channel.fromPath("<s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa>", checkIfExists: true).map{ file -> tuple([id: file.getSimpleName()], file) }.collect()
        }else{

            fasta   = params.fasta ? Channel.fromPath(params.fasta, checkIfExists: true).map{ file -> tuple([id: file.getSimpleName()], file) }.collect()
                                : Channel.fromPath("<s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa>", checkIfExists: true).map{ file -> tuple([id: file.getSimpleName()], file) }.collect()
        }

Hello All, having an out of memory error when running nf-core/serak ipelime on AWS Batch. I am using M5.16large instance types. My command is " nextflow run nf-core/sarek -profile awsbatch,docker --tumor_only true --genome GATK.GRCh38 --awsqueue titan-global-nf-vc-queue --awsregion us-east-1 -params-file nf-params.json" ....in my Job definition I am allocating 195Gibs memory and 64 vCPUs, I am also assigning 16 GBs Memory and 40GB Memory to /tmp. I am getting the Out of memory error below, any Idea what I am doing wrong?

ERROR ~ Error executing process > 'NFCORE_SAREK:sarek:FASTP (Tumor2-1)'

Caused by:
  Essential container in task exited - OutOfMemoryError: Container killed due to memory usage

Command executed:
  [ ! -f  Tumor2-1_1.fastq.gz ] && ln -sf ERR3239286_1.fastq.gz Tumor2-1_1.fastq.gz
  [ ! -f  Tumor2-1_2.fastq.gz ] && ln -sf ERR3239286_2.fastq.gz Tumor2-1_2.fastq.gz
  fastp \
      --in1 Tumor2-1_1.fastq.gz \
      --in2 Tumor2-1_2.fastq.gz \
      --out1 Tumor2-1_1.fastp.fastq.gz \
      --out2 Tumor2-1_2.fastp.fastq.gz \
      --json Tumor2-1.fastp.json \
      --html Tumor2-1.fastp.html \
      \
      \
      \
      --thread 12 \
      --detect_adapter_for_pe \
      --split_by_lines 200000000 --length_required 15 \
      2> >(tee Tumor2-1.fastp.log >&2)

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:sarek:FASTP":
      fastp: $(fastp --version 2>&1 | sed -e "s/fastp //g")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  download failed: <s3://my-ngs-pipline/reads/ERR3239286_1.fastq.gz|s3://my-ngs-pipline/reads/ERR3239286_1.fastq.gz> to ./ERR3239286_1.fastq.gz [Errno 12] Cannot allocate memory
  main: line 283:    83 Killed                  /home/ec2-user/miniconda/bin/aws --region us-east-1 s3 cp --only-show-errors "$source" "$target"

Work dir:
  <s3://my-ngs-pipline/work/1f/4be4cc1a627976ceb01d2170a6ad21|s3://my-ngs-pipline/work/1f/4be4cc1a627976ceb01d2170a6ad21>

Container:
  <http://quay.io/biocontainers/fastp:0.23.4--h5f740d0_0|quay.io/biocontainers/fastp:0.23.4--h5f740d0_0>

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|https://nf-co.re/docs/usage/troubleshooting>

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

ERROR ~ Unexpected error [AbortedException]

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

ERROR ~ Unexpected error while finalizing task 'NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED (wgs_calling_regions_noseconds.hg38)' - cause:

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

Hello, I am having some trouble trying to get this to work so any help would be much appreciated. So for background I have two folders, one with a paired file (A) and another with 20 paired files (B). I have a process which merges the files in folder A with each of the files in folder B. The problem is that I don't always want all 20 files to be merged so I would like to add a function that dictates how many files are merged and I can't figure out how. I have tried the .take and .random functions but all the files in folder B are merged at the end of the process regardless of what function I use. There is no error message because technically the process worked but not as I wanted it to. Can someone please suggest anything to try to fix this? Channel .fromFilePairs("${folder_A}/*_{R1,R2}.fastq") .set { A_pairs } Channel .fromFilePairs("${folder_B}/*_{R1,R2}.fastq") .take(4) .set {B_pairs} process merge { . . . }

Hi everyone, I’m trying to get Nextflow v21 running on my Mac (macOS Sequoia 15, M3 Ultra, ARM64) and I’m open to either: • x86 under Rosetta2, or • native ARM64 My current setup is: 1. Java (x86): OpenJDK 21 installed for x86 with

/usr/local/java21/bin

in my PATH 2. Conda: Miniforge installed under Rosetta2 (crashes on env activation) 3. Docker: Apple‑Silicon Docker Desktop (containers fail to start or hang) If you’ve got Nextflow v21 working on a similar Mac M3 Ultra, could you share: • Java: How you installed/configured JDK for x86 or ARM (Homebrew vs. manual, PATH, etc.) • Conda: Whether you run it under Rosetta2 or natively on ARM, and any stability tweaks • Docker: Platform flags, resource settings or other Docker Desktop tweaks that made it reliable Any pointers, sample configs or scripts would be hugely appreciated! Thanks in advance,

are there any nf-core modules that use the Evo-2 model for pathogenicity prediction on VCFs, perhaps injecting variants into reference and then presenting flanking sequences to the model for inference?

I wonder why singularity cannot access a python script file under scripts/. I'm using:

singularity {
  enabled = true
  autoMounts = true
}

process {
withName:test {container = '<http://quay.io/biocontainers/pandas:2.2.1|quay.io/biocontainers/pandas:2.2.1>'}
}

The error says:

python: can't open file '/nfs/data/test/nf_pipe/scripts/test.py': [Errno 2] No such file or directory

It works fine if I set it to bind the absolute path:

singularity {
  enabled = true
  autoMounts = true
  runOptions = "-B /nfs/"
}

My process file:

process test {
  tag "test"

  input:
  path(genes)
   
  output:
  path("test_out.txt")

  cpus 1
  memory '2 GB'

  script:
  """
  python ${projectDir}/scripts/test.py ${genes}
  """ 
}

This is as expected. What you should do is to put the script in

bin

and call directly (

test.py

rather than

python .../test.py

).

Hi everyone, I'm running nf-core mag 3.3.1 and i keep getting the same warning for gtdbtk. WARN: Unable to stage foreign file: https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz (try 3 of 3) -- Cause: Read data length does not match expected size - bytes read: 1729871529; expected: 108491169765. Why is that? Thanks in advance.

Hi everyone, I'm having some (Docker) container struggles with the local executor (sizeable gcp vm instance). I'm trying to run the nf-core/oncoanalyser pipeline with docker enabled (

docker { enabled = true}

) in my config (latest version/release 2.0.0) but for some reason, the pipeline crashes after staging the files needed, giving me an error that the resource file doesn't exist. The files do exist but they're not owned by my user, but rather by root. This makes the pipeline crash, understandably. What confuses me is why the

docker.enabled = true

is parsed but not the docker profile directives/run options that are provided by default in all nf-core pipelines' nextflow.config (although in this case, the logs clearly state that the nextflow.config has been parsed). This makes the container default to root when running, hence the permission issues. But my question then is, is the only way to enable a profile, in the CLI with the

-profile docker/singularity/etc

argument? I've always enabled my container engine in my config, to make it reusable and shareable so I'm not entirely sure why I'm facing this issue now. It could very well be on my end but I can't seem to pinpoint it. I've also dug into the

.command.run

and the docker run command when the docker profile is enabled/provided in the cli (or when the containerOptions are provided in the config file as such

process.containerOptions = '-u $(id -u):$(id -g)'

) does contain the

'-u $(id -u):$(id -g)'

flag while when I only set the

docker.enabled = true

in my config, the docker run command in the

.command.run

does not contain the appropriate user-related flags (

'-u $(id -u):$(id -g)'

). I've never encountered this issue before (with this pipeline or others, nf-core or not) and I'm very confused. Appreciate any help! 🙂

Hi everyone! I was reading up about the dynamic process resources (https://www.nextflow.io/docs/latest/process.html#dynamic-task-resources) where an example is shown that increases the available memory per task depending on some numeric input parameter, i.e. file size. I was wondering, if its also possible to create some kind of if statement, that will then give the task different amounts of memory, depending on a character input, i.e. the name of a parameter that was specified in the config file and will be passed on to a method in the pipeline (different parameters will cause the method to use more/less memory). Suggestions or hints to an example for this in the documentation are highly appreciated 🙂

Whenever I have two

row.get('', null)

, like below, it emits the `Invalid method invocation `call`` error. It works fine if I remove one of them. Can't figure out why.

Channel
    .fromPath(params.data.sample_sheet, checkIfExists:true)
    .splitCsv(header: true)
    .map { row -> 
           def sample = row.sample
           def read1 = row.read1
           def read2 = row.read2
           def snps = row.snps
           def bam = row.get('bam', null)
           def indels = row.get('indels', null)
           tuple(sample, read1, read2, snps, bam, indels)}
    .set { samples_ch }

With the latest version of nextflow, my CI/CD is failing, has anyone seen something similar:

N E X T F L O W  ~  version 25.03.1-edge
Launching `/home/runner/work/quantms/quantms/main.nf` [cheeky_leakey] DSL2 - revision: 42a6856dbd
Downloading plugin nf-schema@2.3.0
No SDRF given. Using parameters to determine tolerance, enzyme, mod. and labelling settings
WARN: The `when` process section is deprecated -- use conditional logic in the calling workflow instead
[a3/514849] Submitted process > BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK (BSA_design_urls.tsv)
[7a/453be2] Submitted process > BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:PREPROCESS_EXPDESIGN (BSA_design_urls.tsv)
ERROR ~ Failed to publish file: /home/runner/work/quantms/quantms/work/a3/514849ceaaeb22441000a7d82622f1/BSA_design_urls.tsv; to: /home/runner/work/quantms/quantms/test_lfq_docker_results/pipeline_info/BSA_design_urls.tsv [copy] -- See log file for details

 -- Check '.nextflow.log' file for details
ERROR ~ Failed to publish file: /home/runner/work/quantms/quantms/work/a3/514849ceaaeb22441000a7d82622f1/input_check.log; to: /home/runner/work/quantms/quantms/test_lfq_docker_results/pipeline_info/input_check.log [copy] -- See log file for details

 -- 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
-[bigbio/quantms] Pipeline completed with errors-
WARN: Killing running tasks (1)
Error: Process completed with exit code 1.

Does anyone know how to run nextflow using the official docker image? I tried the following command:

docker run --rm \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v $(pwd):/workdir \
  -w /workdir \
  nextflow/nextflow:24.10.6 \
  nextflow run nf-core/rnaseq -profile test,docker --outdir results

Then, it always gives the following error:

Caused by:
  Process `NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (127)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --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:
  127

Command output:
  (empty)

Command error:
  .command.sh: line 8: filter_gtf.py: command not found

Work dir:
  /workdir/work/17/c1a1546534cfc3d7c1e115f3da097e

Container:
  <http://quay.io/biocontainers/python:3.9--1|quay.io/biocontainers/python:3.9--1>

It looks like that the files in the

bin

directory is not mounted to the containers correctly.

Hi, Im trying to figure it out how this error could happen, that the test and the download have different containers:

0s
Run if [ "7" -ne "11" ]; then
  if [ "7" -ne "11" ]; then
    initial_count=7
    final_count=11
    difference=$((final_count - initial_count))
    echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
    tree ./singularity_container_images > ./container_afterwards
    diff ./container_initial ./container_afterwards
    exit 1
  else
    echo "The pipeline can be downloaded successfully!"
  fi
  shell: /usr/bin/bash -e {0}
  env:
    NXF_ANSI_LOG: false
    JAVA_HOME: /opt/hostedtoolcache/Java_Zulu_jdk/17.0.15-6/x64
    JAVA_HOME_17_X64: /opt/hostedtoolcache/Java_Zulu_jdk/17.0.15-6/x64
    CAPSULE_LOG: none
    pythonLocation: /opt/hostedtoolcache/Python/3.12.10/x64
    PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/3.12.10/x64/lib/pkgconfig
    Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.10/x64
    Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.10/x64
    Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.10/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.12.10/x64/lib
4 additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!
4a5
> ├── depot.galaxyproject.org-singularity-bioconductor-msstats-4.10.0--r43hf17093f_0.img
5a7,9
> ├── depot.galaxyproject.org-singularity-pmultiqc-0.0.26--pyhdfd78af_0.img
> ├── depot.galaxyproject.org-singularity-quantms-rescoring-0.0.9--pyhdfd78af_0.img
> ├── depot.galaxyproject.org-singularity-quantms-utils-0.0.21--pyh7e72e81_0.img
10c14
< 1 directory, 7 files
---
> 1 directory, 11 files
Error: Process completed with exit code 1.

I am getting the following error with #C01NHS4CC91 and I don't know the solution. Can someone help me solve it:

Command error:
  WARNING: Not virtualizing pid namespace by configuration
  Using GATK jar /opt/conda/share/gatk4-4.6.1.0-0/gatk-package-4.6.1.0-local.jar
  Running:
      java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4915M -XX:-UsePerfData -jar /opt/conda/share/gatk4-4.6.1.0-0/gatk-package-4.6.1.0-local.jar BedToIntervalList --INPUT fish6_annotation.exon.bed --OUTPUT fish6_annotation.interval_list --SEQUENCE_DICTIONARY NHGRI_Fish6_cons.dict --TMP_DIR . --DROP_MISSING_CONTIGS TRUE
  16:12:43.012 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/share/gatk4-4.6.1.0-0/gatk-package-4.6.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
  [Tue Apr 29 16:12:43 GMT 2025] BedToIntervalList --INPUT fish6_annotation.exon.bed --SEQUENCE_DICTIONARY NHGRI_Fish6_cons.dict --OUTPUT fish6_annotation.interval_list --DROP_MISSING_CONTIGS true --TMP_DIR . --SORT true --UNIQUE false --KEEP_LENGTH_ZERO_INTERVALS false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
  [Tue Apr 29 16:12:43 GMT 2025] Executing as okendojo@cn0040 on Linux 4.18.0-425.19.2.el8_7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.11-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.6.1.0
  SLF4J(W): Class path contains multiple SLF4J providers.
  SLF4J(W): Found provider [org.apache.logging.slf4j.SLF4JServiceProvider@65cc5252]
  SLF4J(W): Found provider [ch.qos.logback.classic.spi.LogbackServiceProvider@42c12b3e]
  SLF4J(W): See <https://www.slf4j.org/codes.html#multiple_bindings> for an explanation.
  SLF4J(I): Actual provider is of type [org.apache.logging.slf4j.SLF4JServiceProvider@65cc5252]
  [Tue Apr 29 16:12:44 GMT 2025] picard.util.BedToIntervalList done. Elapsed time: 0.02 minutes.
  Runtime.totalMemory()=1136656384
  To get help, see <http://broadinstitute.github.io/picard/index.html#GettingHelp>
  picard.PicardException: Start on sequence 'chr20' was past the end: 59305174 < 59340857
  	at picard.util.BedToIntervalList.doWork(BedToIntervalList.java:169)
  	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
  	at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
  	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
  	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
  	at org.broadinstitute.hellbender.Main.main(Main.java:306)

Work dir:
  /vf/users/okendojo/zebrafish/data/g3/F2_variants/work/20/49012642ceaa8bef2bf22488e1512b

Container:
  /data/okendojo/nxf_singularity_cache/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-b2-b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98-data.img

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- 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

executor >  slurm (7)
[fc/be6894] NFC…Y (NHGRI_Fish6_cons.fasta) | 1 of 1 ✔
[71/5d2097] NFC…BED (fish6_annotation.gtf) | 1 of 1 ✔
[cf/d187d7] NFC…REGIONS (fish6_annotation) | 1 of 1 ✔
[-        ] NFC…ME:BGZIPTABIX_KNOWN_INDELS -
[-        ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[0f/39dc8d] NFC…X (NHGRI_Fish6_cons.fasta) | 1 of 1 ✔
[-        ] NFC…NAVAR:PREPARE_GENOME:UNTAR -
[9a/89e467] NFC…E_GENOME:STAR_INDEXVERSION | 1 of 1 ✔
[-        ] NFC…GENOME:STAR_GENOMEGENERATE -
[-        ] NFC…E_ALIGNMENT:SAMTOOLS_INDEX -
[d0/9874b3] NFC…:CAT_FASTQ (grandchildren) | 1 of 1 ✔
[-        ] NFCORE_RNAVAR:RNAVAR:FASTQC    -
[20/490126] NFC…VALLIST (fish6_annotation) | 1 of 1, failed: 1 ✘
[-        ] NFC…AR:GATK4_INTERVALLISTTOOLS -
[-        ] NFC…ASTQ_ALIGN_STAR:STAR_ALIGN -
[-        ] NFC…TOOLS_GENOME:SAMTOOLS_SORT -
[-        ] NFC…OOLS_GENOME:SAMTOOLS_INDEX -
[-        ] NFC…TS_SAMTOOLS:SAMTOOLS_STATS -
[-        ] NFC…SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] NFC…SAMTOOLS:SAMTOOLS_IDXSTATS -
Plus 22 more processes waiting for tasks…
-[nf-core/rnavar] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_RNAVAR:RNAVAR:GATK4_BEDTOINTERVALLIST (fish6_annotation)'