Description of the bug

A USER ERROR has occurred: Bad input: Sample P-*_P-*-REF-100X is not in BAM header: [_P--REF-100X,_-TMN-150X]````
I have the same error as the issue : https://github.com/nf-core/sarek/issues/7322, I added in my .config:

 withName: 'MUTECT2_PAIRED' {
      ext.args = { "<copy ext.args from modules.config to avoid overwritting>  --normal-sample ${meta.normal_id}" }
   }

, nothing changes.

Command used and terminal output

Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (P-*-TMN-150X_vs_P-*-REF-100X)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED (P-*-TMN-150X_vs_*-REF-100X)` terminated with an error exit status (2)


Command executed:

  gatk --java-options "-Xmx32768M -XX:-UsePerfData" \
      Mutect2 \
      --input P-*.recal.cram --input P-*.recal.cram \
      --output P-*-TMN-150X_vs_P-*-REF-100X.mutect2.vcf.gz \
      --reference Homo_sapiens_assembly38.fasta \
      --panel-of-normals 1000g_pon.hg38.vcf.gz \
      --germline-resource af-only-gnomad.hg38.vcf.gz \
      --intervals chr1_69066-70033.bed \
      --tmp-dir . \
      --f1r2-tar-gz P-NI62112-TMN-150X_vs_P-NI62112-REF-100X.mutect2.f1r2.tar.gz --normal-sample P-*_P-*-REF-100X
  
  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

------------------------------------------------
nextflow run nf-core/sarek \
    -c config/nf_core_sarek.config \
    -profile singularity \
    --input  config/samplesheet_wes_mapped.csv \
    --outdir results/nfcore_sarek/WES/ \
    --intervals resources/Homo_sapiens/target_files/twist_human_core_exome_and_integragen_custom_v2.bed \
    --wes \
    --monochrome_logs \
    -ansi-log false \
    -params-file config/nf_core_sarek_params.yaml  \
    -resume \
    -with-report  results/nfcore_sarek/WES/report.html/ \
    -with-timeline results/nfcore_sarek/WES/timeline.html \
    -process.errorStrategy 'retry' 
    -process.maxRetries 5

Relevant files

Using GATK jar /usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx32768M -XX:-UsePerfData -jar /usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar Mutect2 --input P--REF-100X.recal.cram --input P-MA2121-TMN-150X.recal.cram --output P--TMN-150X_vs_P--REF-100X.mutect2.vcf.gz --reference Homo_sapiens_assembly38.fasta --panel-of-normals 1000g_pon.hg38.vcf.gz --germline-resource af-only-gnomad.hg38.vcf.gz --intervals chr1_69066-70033.bed --tmp-dir . --f1r2-tar-gz P--TMN-150X_vs_P--REF-100X.mutect2.f1r2.tar.gz --normal-sample P-_P-*-REF-100X
10:17:51.899 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:17:52.259 INFO Mutect2 - ------------------------------------------------------------
10:17:52.267 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.5.0.0
10:17:52.267 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
10:17:52.268 INFO Mutect2 - Executing as v_robin@n11 on Linux v3.10.0-957.27.2.el7.x86_64 amd64
10:17:52.268 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v17.0.10-internal+0-adhoc..src
10:17:52.268 INFO Mutect2 - Start Date/Time: September 18, 2024 at 10:17:51 AM GMT
10:17:52.268 INFO Mutect2 - ------------------------------------------------------------
10:17:52.269 INFO Mutect2 - ------------------------------------------------------------
10:17:52.270 INFO Mutect2 - HTSJDK Version: 4.1.0
10:17:52.270 INFO Mutect2 - Picard Version: 3.1.1
10:17:52.270 INFO Mutect2 - Built for Spark Version: 3.5.0
10:17:52.271 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:17:52.271 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:17:52.272 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:17:52.272 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:17:52.272 INFO Mutect2 - Deflater: IntelDeflater
10:17:52.273 INFO Mutect2 - Inflater: IntelInflater
10:17:52.273 INFO Mutect2 - GCS max retries/reopens: 20
10:17:52.273 INFO Mutect2 - Requester pays: disabled
10:17:52.274 INFO Mutect2 - Initializing engine
10:17:54.653 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/beegfs/scratch/v_robin/.tmp/nxf.PVfwj5aNd0/1000g_pon.hg38.vcf.gz
10:17:55.230 INFO FeatureManager - Using codec VCFCodec to read file file:///mnt/beegfs/scratch/v_robin/.tmp/nxf.PVfwj5aNd0/af-only-gnomad.hg38.vcf.gz
10:17:55.540 INFO FeatureManager - Using codec BEDCodec to read file file:///mnt/beegfs/scratch/v_robin/.tmp/nxf.PVfwj5aNd0/chr1_69066-70033.bed
10:17:56.168 INFO IntervalArgumentCollection - Processing 43826111 bp from intervals
10:17:56.400 INFO Mutect2 - Done initializing engine
10:17:56.519 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
10:17:56.548 INFO NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
10:17:56.553 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
10:17:56.577 INFO Mutect2 - Shutting down engine
[September 18, 2024 at 10:17:56 AM GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1157627904

A USER ERROR has occurred: Bad input: Sample P-_P--REF-100X is not in BAM header: [_P--REF-100X, _P--TMN-150X]

System information

Version nf-core sarek 3.4.3
Container Singularity
Executor slurm
Hardware HPC
version nextflow 24.04.4