Somatic tumor-normal run with indexcov fails at SAMTOOLS_REINDEX_BAM due to tuple mismatch

[lucafagnocchi]

Description of the bug

Hi nf-core/sarek team,

I am running a paired tumor-normal somatic analysis with nf-core/sarek 3.9.0. The pipeline fails when indexcov is included in --tools. The failure occurs in the somatic indexcov branch at:

NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_INDEXCOV:SAMTOOLS_REINDEX_BAM

The error is:

Input tuple does not match tuple declaration in process
`NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_INDEXCOV:SAMTOOLS_REINDEX_BAM`

The offending value is a paired tumor-normal tuple containing the pair metadata plus both the normal and tumor CRAM/CRAI files:

[
  [
    id: xxx-T_vs_xxx-N,
    normal_id: xxx-N,
    patient: xxx,
    sex: XY,
    tumor_id: xxx-T,
    contamination: null
  ],
  /.../xxx-N.recal.cram,
  /.../xxx.recal.cram.crai,
  /.../xxx-T.recal.cram,
  /.../xxx-T.recal.cram.crai
]

This looks like the somatic paired CRAM tuple is being passed directly into SAMTOOLS_REINDEX_BAM, but the process declaration expects a different tuple shape.

Command used and terminal output

nextflow run nf-core/sarek \
  -r 3.9.0 \
  -profile alliance_canada \
  -c sarek_nibi_somatic_nextflow_RESUME_FIX.config \
  -params-file sarek_nibi_somatic_params.yml \
  --input samplesheet.somatic.xxx-T_vs_N.csv \
  --outdir /path/to/output/somatic \
  --genome GATK.GRCh38 \
  --fasta /path/to/Homo_sapiens_assembly38.masked_nonACGT_to_N.fasta \
  --fasta_fai /path/to/Homo_sapiens_assembly38.masked_nonACGT_to_N.fasta.fai \
  --dict /path/to/Homo_sapiens_assembly38.masked_nonACGT_to_N.dict \
  --tools freebayes,mutect2,muse,strelka,manta,tiddit,indexcov,ascat,cnvkit,controlfreec,msisensorpro,ngscheckmate,snpeff,vep,merge \
  --only_paired_variant_calling \
  --filter_vcfs \
  --normalize_vcfs \
  --snv_consensus_calling \
  --consensus_min_count 2 \
  --save_reference

Relevant files

Relevant log output

DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_INDEXCOV:SAMTOOLS_REINDEX_BAM (1); work-dir=null

error [nextflow.exception.ProcessUnrecoverableException]:
Input tuple does not match tuple declaration in process
`NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_INDEXCOV:SAMTOOLS_REINDEX_BAM`

offending value:
[
  [
    id:xxx-T_vs_xxx-N,
    normal_id:xxx-N,
    patient:xxx,
    sex:XY,
    tumor_id:xxx-T,
    contamination:null
  ],
  /.../xxx-N.recal.cram,
  /.../xxx-N.recal.cram.crai,
  /.../xxx-T.recal.cram,
  /.../xxx-T.recal.cram.crai
]

System information

Pipeline: nf-core/sarek
Version: 3.9.0
Nextflow: 26.04.4
Profile: alliance_canada
Cluster: DRAC/Nibi
Executor: Slurm
Container engine reported by Nextflow: singularity/apptainer via Alliance Canada profile
Analysis type: paired tumor-normal somatic
Input type: FASTQ samplesheet with matched normal and tumor
Reference: GATK.GRCh38, with local masked FASTA/FAI/dict overrides