Error executing process > 'NFCORE_RNAFUSION:DEMUX_FROM_RUNDIR:DEMULTIPLEX:SAMPLESHEET_CHECK (20260226_LH00995_0015_B23MHV2LT4)'

Caused by:
  Process `NFCORE_RNAFUSION:DEMUX_FROM_RUNDIR:DEMULTIPLEX:SAMPLESHEET_CHECK (20260226_LH00995_0015_B23MHV2LT4)` terminated with an error exit status (1)


Command executed:

  mkdir -p merged/Reports
  
  first=true
  for f in ds*/*; do
      if [ "$first" = true ]; then
          cat "$f" > merged/Reports/Demultiplex_Stats.csv
          first=false
      else
          tail -n+2 "$f" >> merged/Reports/Demultiplex_Stats.csv
      fi
  done
  
  if ls tu*/* 1>/dev/null 2>&1; then
      first=true
      for f in tu*/*; do
          if [ "$first" = true ]; then
              cat "$f" > merged/Reports/Top_Unknown_Barcodes.csv
              first=false
          else
              tail -n+2 "$f" >> merged/Reports/Top_Unknown_Barcodes.csv
          fi
      done
  fi
  
  sample_sheet_qc.py \
      merged \
      --fail-threshold 0.1 --warning-threshold 5.0 --non-ntc-threshold 1000000 --ntc-threshold 500000 \
      --output-dir . \
      --create-pass-file
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAFUSION:DEMUX_FROM_RUNDIR:DEMULTIPLEX:SAMPLESHEET_CHECK":
      sample_sheet_qc: 1.1.0
  END_VERSIONS

Command exit status:
  1

Command output:
  Error: fail_threshold must be greater than warning_threshold

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/30f08445b8b9cbfc5b18625016764b

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/samplesheet_check:1.1.0

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`