Hi there, I am coming from #C043FMKUNLB channel. 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. Also

GRCh37

as reference genome instead of GRCh38. 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. 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

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

Just to note that I made some suggestions in the #C043FMKUNLB question, so anyone looking to answer it may be already answered 😉

Thanks! Basically I was using an old config file with

-c

, I removed this option and use

-params-file

to specify parameters.

-c

is used only for nextflow option. Also use the last updated sarek version. Sarek run without problems with my data, and I can find the bam file in

works/

directory which is a great new! However the annotated vcf is not here, probably because I did not specified the tools to use for the variant calling and annotation steps. Also if I want a bam file in my output directory instead of work I guess I am supposed to use

"save_mapped": true

in params file. I run with

-resume

but I am not able to debug the error I get. Here the command:

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/ -r 3.8.1 -with-report -with-trace -with-timeline -with-dag -params-file ipa_params.json -resume

The sample sheet (with one tumor sample specified with status 1):

cat samplesheet_mapping_NGShem.csv

patient,sex,status,sample,lane,fastq_1,fastq_2
C2508328-star,NA,1,C2508328-star,L1,/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

The params file:

cat ipa_params.json

{
  "igenomes_ignore": true,
  "genome": "GATK.GRCh37",
  "markdup_java_options": "-Xmx20g",
  "umi_read_structure": "5M2S+T 5M2S+T",
  "tools": "mutect2,mpileup,vep",
  "annotation-cache": "/mnt/ARC/IPA/CBIOMOL_ARCH/References/vep/",
  "dbsnp": "/mnt/HDD2/sarek_inhouse/bgzip_input/dbsnp_138.b37.vcf.gz",
  "intervals": "/mnt/ARC/IPA/CBIOMOL_ARCH/MISEQ_bioinfo/Heme.panel/Annotation/HemePanel.padded.Nochr.v4.bed",
  "known_indels": "/mnt/HDD2/sarek_inhouse/bgzip_input/1000G_phase1.indels.b37.vcf.gz",
  "known_snps": "/mnt/HDD2/sarek_inhouse/bgzip_input/1000G_phase1.snps.high_confidence.b37.vcf.gz",
  "pon": "/mnt/HDD2/sarek_inhouse/bgzip_input/MuTect2_PON.vcf.gz",
  "max_cpus": 24,
  "max_memory": "128 GB"
}

And the specific error and the log joined:

nextflow.exception.WorkflowScriptErrorException: The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : mutect2

I looked for this error on slack research bar. In a 24/09/2025 topic, it seems it was a question of sarek version. As your advice, I am using the last one

-r 3.8.1

. So I am wondering how to fix that and currently have no idea. Is there somewhere a params file with all possible argument? It could be useful. Best, Vimel

Hiya. For sarek 3.9.0dev, I had the same tumour/mutect error when I changed something completely unrelated yesterday - . (in the UMI workflow). Seemed to be caused by my changes to that upstream workflow not working properly...and terminating there (all fine when UMI workflow corrected). Assuming the mutect error was a knock-on effect ...but obviously not very informative/helpful...for me at least.

I made changes in the params file (hg38 reference genome, good vep location, freebayes, mpileup and manta). It is currently running without Mutect2 only, otherwise I have the same error. I think there is a problem with Mutect2 which cannot handle a sample sheet with only a tumor only? Or something more complex but linked to Mutect2