Hi, I am trying to do joint calling with Mutect2 for all these samples and the joint calling is instead split in two subgroups. Running sarek v3.7.1

cat samplesheet.csv

patient,sex,status,sample,lane,fastq_1,fastq_2

JEA,XY,1,JEA_665_BMO_T4_1ng,1,inp/Exome/Necker_Nextseq_run1132/665_BMO_T4_1ng_S1_L001_R1_001.fastq.gz,inp/Exome/Necker_Nextseq_run1132/665_BMO_T4_1ng_S1_L001_R2_001.fastq.gz

JEA,XY,1,JEA_665_BO_1ng,1,inp/Exome/Necker_Nextseq_run1132/665_BO_1ng_S1_L001_R1_001.fastq.gz,inp/Exome/Necker_Nextseq_run1132/665_BO_1ng_S1_L001_R2_001.fastq.gz

JEA,XY,1,JEA_665_SANG_1ng,1,inp/Exome/Necker_Nextseq_run1132/665_SANG_1ng_S1_L001_R1_001.fastq.gz,inp/Exome/Necker_Nextseq_run1132/665_SANG_1ng_S1_L001_R2_001.fastq.gz

JEA,XY,1,JEA_667_BMO_T4_1ng,1,inp/Exome/Necker_Nextseq_run1132/667_BMO_T4_1ng_S1_L001_R1_001.fastq.gz,inp/Exome/Necker_Nextseq_run1132/667_BMO_T4_1ng_S1_L001_R2_001.fastq.gz

JEA,XY,1,JEA_667_BO_1ng,1,inp/Exome/Necker_Nextseq_run1132/667_BO_1ng_S1_L001_R1_001.fastq.gz,inp/Exome/Necker_Nextseq_run1132/667_BO_1ng_S1_L001_R2_001.fastq.gz

JEA,XY,1,JEA_667_SANG_1ng,1,inp/Exome/Necker_Nextseq_run1132/667_SANG_1ng_S1_L001_R1_001.fastq.gz,inp/Exome/Necker_Nextseq_run1132/667_SANG_1ng_S1_L001_R2_001.fastq.gz

JEA,XY,1,JEA_DIAG_1ng,1,inp/Exome/Necker_Nextseq_run1132/JEAN_DIAG_1ng_S1_L001_R1_001.fastq.gz,inp/Exome/Necker_Nextseq_run1132/JEAN_DIAG_1ng_S1_L001_R2_001.fastq.gz

JEA,XY,1,JEA_DIAG_200ng,1,inp/Exome/Necker_Nextseq_run1132/JEAN_DIAG_200_S1_L001_R1_001.fastq.gz,inp/Exome/Necker_Nextseq_run1132/JEAN_DIAG_200_S1_L001_R2_001.fastq.gz

zcat results/annotation/mutect2/JEA/JEA.mutect2.filtered_snpEff_VEP.ann.vcf.gz | grep tumor_sample
##tumor_sample=JEA_JEA_667_BO_1ng
##tumor_sample=JEA_JEA_667_SANG_1ng
##tumor_sample=JEA_JEA_DIAG_1ng

I see two running jobs for JEA that will produce results to the same filepath. If I remove the first vcf produced, I will get the vcf for the remaining samples :

[1e/3367b6] NFCORE_SAREK:sarek:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2:MUTECT2 (JEA)    [ 50%] 1 of 2, cached: 1

cat nf-params.json
{
    "input": "samplesheet.csv",
    "outdir": "results",
    "wes": true,
    "intervals": "inp/bed/S31285117_Padded.bed",
    "tools": "mutect2,merge",
    "trim_fastq": true,
    "joint_germline": false,
    "joint_mutect2": true
}