Mutect2 run only on one intervals file

[ekushele]

Description of the bug

Hi,

I'm trying to run sarek with "mutect2" for variant calling. Pipeline completes successfully, but the folder "output/variant_calling/" is empty. It seems like process MUTECT2_PAIRED run only on one interval file, the .command.sh is:

#!/bin/bash -euo pipefail
gatk --java-options "-Xmx29491M -XX:-UsePerfData" \
    Mutect2 \
    --input 1641_parp_ov.recal.cram --input FFPE_ovary.recal.cram \
    --output FFPE_ovary_vs_1641_parp_ov.mutect2.chr2_16146120-32867130.vcf.gz \
    --reference Homo_sapiens_assembly38.fasta \
    --panel-of-normals 1000g_pon.hg38.vcf.gz \
    --germline-resource af-only-gnomad.hg38.vcf.gz \
    --intervals chr2_16146120-32867130.bed \
    --tmp-dir . \
    --f1r2-tar-gz FFPE_ovary_vs_1641_parp_ov.mutect2.chr2_16146120-32867130.f1r2.tar.gz --normal-sample OV3_1641_parp_ov

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED":
    gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
END_VERSIONS

I think it should run on all bed files combined together or run on all bed files and then combine them together...

Command used and terminal output

nextflow -config config_sarek.conf run -resume -params-file new_OV3_params.yaml  -profile singularity nf-core/sarek

new_OV3_params.yaml file:
input: new_OV3_sample_sheet.csv
outdir: new_output
step: mapping
wes: true
tools: 'mutect2,vep'
genome: GATK.GRCh38
save_reference: true
download_cache: true


new_OV3_sample_sheet.csv:
patient,sex,status,sample,lane,fastq_1,fastq_2
OV3,XX,1,FFPE_ovary,lane_1,fastq/OV3_FFPE_ovary_R1.conc.fastq.gz,fastq/OV3_FFPE_ovary_R2.conc.fastq.gz
OV3,XX,0,1641_parp_ov,lane_1,fastq/1641_parp_ov_S4_R1_001.fastq.gz,fastq/1641_parp_ov_S4_R2_001.fastq.gz

Relevant files

No response

System information

nextflow version: 23.04.4 nf-core/sarek: 3.4.1

[maxulysse]

Can you try again with 3.4.2?

[FriederikeHanssen]

Is this a persisting issue? From looking at the full size test, we see that Mutect2 runs on each interval separately and they are then joined together: https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/3NvYfMZddVVDCY