Hi there, I ran sarek with

test_full

few days ago and it worked perfectly:

nextflow run nf-core/sarek -r 3.8.1 -profile singularity,test_full --outdir /mnt/HDD2/sarek_test/output/ -resume

[...]
-[nf-core/sarek] Pipeline completed successfully-

Completed at: 13-Feb-2026 21:58:44
Duration    : 4h 52m 59s
CPU hours   : 96.3 (42,1% cached)
Succeeded   : 214
Cached      : 48

Then I tried to run it with our data by starting with one patient with paired-end fastq files (already demultiplexed and merged). I recycled the

base.config

found in your git and add the

umi_read_structure

and

umi_in_read_header

to force fgbio step. However I am stuck at

bwa-mem

step (which was not the case without UMI information):

nextflow run nf-core/sarek -profile singularity --input /mnt/HDD2/sarek_inhouse/samplesheet_mapping_NGShem.csv --outdir /mnt/HDD2/sarek_inhouse/2026-02-04_SRP_NGShem/ -c /mnt/HDD2/sarek_inhouse/base.config -r 3.8.0

[...]
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/sarek] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_SAREK: SAREK :FASTQ_PREPROCESS_GATK:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:ALIGN_UMI:BWAMEM1_MEM (C2508328-star-lane_1)'

Caused by:
  No signature of method: nextflow.processor.TaskPath.get() is applicable for argument types: (Integer) values: [0]
  Possible solutions: getAt(int), grep(), getAt(java.lang.String), grep(java.lang.Object), head(int), wait() -- Check script '/home/localadmin/.nextflow/assets/nf-core/sarek/modules/nf-core/bwa/mem/main.nf' at line: 29

Source block:
  def args = task.ext.args ?: ''
  def args2 = task.ext.args2 ?: ''
  def prefix = task.ext.prefix ?: "${meta.id}"
  def samtools_command = sort_bam ? 'sort' : 'view'
  def extension = args2.contains("--output-fmt sam")   ? "sam" :
                  args2.contains("--output-fmt cram")  ? "cram":
                  sort_bam && args2.contains("-O cram")? "cram":
                  !sort_bam && args2.contains("-C")    ? "cram":
                  "bam"
  def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
  if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
  """
  INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
  
  bwa mem \\
      $args \\
      -t $task.cpus \\
      \$INDEX \\
      $reads \\
      | samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} -
  
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
      bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
      samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
  END_VERSIONS
  """

Container:
  /mnt/HDD2/sarek_inhouse/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-bf-bf7890f8d4e38a7586581cb7fa13401b7af1582f21d94eef969df4cea852b6da-data.img

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
WARN: Failed to render execution report -- see the log file for details
WARN: Failed to render execution timeline -- see the log file for details

If I understand well the error is due to an non-existent prefix value:

~/.nextflow/assets/nf-core/sarek/modules/nf-core/bwa/mem/main.nf

def prefix = task.ext.prefix ?: "${meta.id}"

Do you know how to define prefix? I thought it was taken from the patient +/- combination lane from the sample sheet. I tried to force a value on

-c .config

file under

params

or

process

but as I am a beginner on nextflow I may miss something. Here the sample sheet:

cat samplesheet_mapping_NGShem.csv

patient,sex,status,sample,lane,fastq_1,fastq_2
C2508328-star,NA,1,C2508328-star,lane_1,/mnt/SHARE_NGSDATA/IPA_NHE/260204_VH01811_146_AAHJLJCM5/Analysis/1/Data/fastq/C2508328-star_S1_R1_001.fastq.gz,/mnt/SHARE_NGSDATA/IPA_NHE/260204_VH01811_146_AAHJLJCM5/Analysis/1/Data/fastq/C2508328-star_S1_R2_001.fastq.gz

I also joined the log file and base.config. The nextflow version used is 25.10.3 and the sarek version used is 3.8.0. I tried to find this error on slack search bar but I was not able to found something similar. Hope you have enough information to give me some hints. Thanks for your time and help. Best, Vimel

The offending line is

def prefix = task.ext.prefix ?: "${meta.id}"

. The ID is generated from the sample sheet, so I recommend checking your sample names. It may be that

C2508328-star-lane_1

doesn’t work as prefix due to the underscore or hyphens? In case that didn’t help, mind that there is a dedicated channel #CGFUX04HZ for pipeline-specific questions. Lastly, mind that you are running 3.8.0 now and did run 3.8.1 for the test, so that is not entirely the same pipeline.

Hi Matthias, thanks for your fast reply. I will give a try without "-". I already give a try with LANE instead of lane_1 but did not work. I will rename

C2508328-star

to

C2508328star

. Thanks! However the prefix exists when I check the command:

singularity run --bind /mnt/HDD2/sarek_inhouse/ /mnt/HDD2/sarek_inhouse/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-bf-bf7890f8d4e38a7586581cb7fa13401b7af1582f21d94eef969df4cea852b6da-data.img

Singularity> cd /mnt/HDD2/sarek_inhouse/work/b0/44a5b97d596779ab2b496505aca785/
Singularity> cat .command.sh
#!/bin/bash -euo pipefail
samtools \
    bam2fq \
    -T RX \
    -@ 2 \
    C2508328-star-lane_1.bam | gzip --no-name > C2508328-star-lane_1_interleaved.fq.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:sarek:FASTQ_PREPROCESS_GATK:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:BAM2FASTQ":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS

It is my first post, good to know for #CGFUX04HZ channel I will post on it if I am still stuck! Best, Vimel

🤔 You are right, I probably deceived you here with some irrelevant suggestion. Sorry. The rationale was that the prefix in this module is outputted without quotes, so the CLI argument parser of

bwa mem

or

samtools

might happily mistake part of your ID it for another command line argument and parse it as

-o C2508328 -s tar -l ane_1.bam

or the like:

bwa mem \\
      $args \\
      -t $task.cpus \\
      \$INDEX \\
      $reads \\
      | samtools $samtools_command $args2 ${reference} --threads $task.cpus -o ${prefix}.${extension} -

Just a shot into the dark though, so best to ask in #CGFUX04HZ.

Thanks Matthias! Your first clue was also a good one to try. I will post my problem on the correct channel. Thanks again.

Don't use a config file to pass parameters, use a params.json file if you want to do that.

I will try that thanks.

That may be part of the issue. The other question, is where did you get that base.config that you've modified? It contains e.g.

max_cpus

that hasn't been in sarek for some time

This one: https://github.com/nf-core/sarek/blob/master/conf/base.config (3 months ago old)

uhh, almost nothing is in common between that file and the one you used?