I've been trying to run a

test_full

with nf-sarek master and the k8s executor and I'm running into the following error:

Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH (HCC1395T_vs_HCC1395N)` terminated with an error exit status (1)


Command executed:

  cnvkit.py \
      batch \
      HCC1395T.bam \
      --normal HCC1395N.bam \
      --fasta Homo_sapiens_assembly38.fasta \
       \
      --targets S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed \
      --processes 6 \
      --method hybrid --diagram --scatter

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH":
      cnvkit: $(cnvkit.py version | sed -e 's/cnvkit v//g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Processing reads in HCC1395N.bam
  [E::hts_idx_load3] Could not load local index file 'HCC1395N.bam.bai' : No such file or directory
  [E::hts_idx_load3] Could not load local index file 'HCC1395N.bam.bai' : No such file or directory
  Processing reads in HCC1395N.bam
  Time: 10.182 seconds (0 reads/sec, 4128 bins/sec)
  Summary: #bins=42032, #reads=0, mean=0.0000, min=0.0, max=0.0
  Percent reads in regions: 0.000 (of 154340066 mapped)
  Wrote ./HCC1395N.antitargetcoverage.cnn with 42032 regions

The YAML for my Nextflow pod is:

apiVersion: v1
kind: Pod
metadata:
  name: nextflow-testrun
  namespace: nextflow
spec:
  containers:
    - name: nextflow-testrun
      image: docker.io/nextflow/nextflow:25.10.4
      command:
        - bash
        - -c
        - time nextflow -c /conf/nextflow.config run nf-core/sarek -profile test_full --outdir /pvc/outdir -work-dir /pvc/workdir
      volumeMounts:
        - name: nextflow-conf
          mountPath: /conf
        - name: nextflow-data
          mountPath: /pvc
          subPath: test
      env:
        - name: NXF_HOME
          value: /pvc/nxf_home
  volumes:
    - name: nextflow-conf
      configMap:
        name: nextflow-config
        optional: false
    - name: nextflow-data
      persistentVolumeClaim:
        claimName: testclaim
  restartPolicy: Never
  serviceAccountName: nextflow

And my

nextflow.config

is:

process {
    executor = 'k8s'
}

k8s {
    storageClaimName = 'testclaim'
    storageMountPath = '/pvc'
    storageSubPath = 'test'
    namespace = 'nextflow'
    serviceAccount = "nextflow"
}

process {
  # Halve cpu requests (not included in this message)
}