Some issues caused an error in the variant_calling step: There are multiple input files for each of the following file names

[hsk6328]

Description of the bug

Hello, I am very grateful for your development of the Sarek pipeline. This pipeline has been very helpful to me in handling WGS analysis. However, I encountered an error when testing the pipeline with the test dataset. I would like to ask what might have caused this error.

When I provide a pair of normal and tumor data, an error occurs when calling BAM_VARIANT_CALLING_SOMATIC_ALL in the variant_calling step. The error message is as follows:

ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:CAT_MPILEUP (1)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:CAT_MPILEUP` input file name collision -- There are multiple input files for each of the following file names: HCC1395T_vs_HCC1395N.mpileup.gz


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

And this is the sample.stomatic.csv:

patient,sex,status,sample,lane,fastq_1,fastq_2
HCC1395,XX,0,HCC1395N,1,./SRR7890919.10M_1.fastq.gz,./SRR7890919.10M_2.fastq.gz
HCC1395,XX,1,HCC1395T,1,./SRR7890918.10M_1.fastq.gz,./SRR7890918.10M_2.fastq.gz

This is the configuration file that I set up, with other parameters kept at default values:

params {
    config_profile_name        = 'WES Demo'
    max_cpus   = 8

    input = '/mnt/disk0/01.nf-core-pipelines/demo/sarek_3.4.0/wes.demo/sample.stomatic.csv'

    // Other params
    tools       = 'controlfreec,vep'
    split_fastq = 20000000
    intervals   = '/mnt/disk0/01.nf-core-pipelines/demo/sarek_3.4.0/wes.demo/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
    wes         = true
}

Could you please provide valuable suggestions for this runtime error? Thank you very much!

Command used and terminal output

nextflow run ${nfcorePath}/nf-core-sarek_3.4.0/3_4_0 -profile singularity -c wes.conf --outdir ./outdir --genome GATK.GRCh38

Relevant files

nextflow.log

System information

• Nextflow version: 23.10.1 build 5891
• System: Linux 3.10.0-1160.108.1.el7.x86_64
• Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 11.0.22+7-LTS
• Encoding: UTF-8 (ANSI_X3.4-1968)
• Version of nf-core/sarek (3.4.0)