Workflow validation fail with secondaryFiles

[r78v10a07]

I have a tool:

cwlVersion: v1.2
class: CommandLineTool

label: Samtools-index-bam
doc: Samtools is a suite of programs for interacting with high-throughput sequencing data

requirements:
  InlineJavascriptRequirement: {}
  InitialWorkDirRequirement:
    listing:
      - $(inputs.bam)

hints:
  - $import: samtools-docker.yml
  - $import: samtools-bioconda.yml

inputs:
  bam:
    type: File
    inputBinding:
      position: 1

outputs:
  indexed_bam:
    type: File
    secondaryFiles: .bai
    outputBinding:
      glob: $(inputs.bam.basename)

baseCommand: [samtools, index, -b]

The workflow:

class: Workflow
cwlVersion: v1.2

id: bwa_alignment_sort
doc: This workflow aligns the fastq files using bwa, sort and index the BAM file
label: bwa alignment workflow

requirements:
  InlineJavascriptRequirement: {}
  StepInputExpressionRequirement: {}
  SubworkflowFeatureRequirement: {}

inputs:
  bam: File
  threads: int

outputs:
  sorted_indexed_bam:
    outputSource: bam_index/indexed_bam
    type: File
    secondaryFiles: .bai

steps:
  bam_sort:
    run: ../../tools/samtools/samtools-sort.cwl
    label: Samtools-sort
    in:
      in_bam: bam
      out_bam:
        valueFrom: ${ return inputs.in_bam.nameroot.replace('Aligned.out', '') + "_sorted.bam";}
      threads: threads
    out: [out_sam]
  bam_index:
    run: ../../tools/samtools/samtools-index-bam.cwl
    label: Samtools-index
    in:
      bam: bam_sort/out_sam
    out: [indexed_bam]

I'm getting this error:

(cwltool) hydra:Variant-calling> cwltool --debug --validate samtools-sort_index.cwl
INFO /opt/miniconda3/envs/cwltool/bin/cwltool 3.1.20250715140722
INFO Resolved 'samtools-sort_index.cwl' to 'file:///Users/veraalva/Work/Developer/Python/cwl-ngs-workflows-cbb/workflows/Variant-calling/samtools-sort_index.cwl'
ERROR I'm sorry, I couldn't load this CWL file.
The error was:
Traceback (most recent call last):
  File "cwltool/main.py", line 1134, in main
  File "cwltool/load_tool.py", line 588, in make_tool
  File "cwltool/workflow.py", line 44, in default_make_tool
  File "cwltool/workflow.py", line 125, in __init__
  File "cwltool/checker.py", line 185, in static_checker
  File "cwltool/checker.py", line 429, in _check_all_types
  File "cwltool/checker.py", line 37, in check_types
  File "cwltool/checker.py", line 88, in can_assign_src_to_sink
TypeError: list object expected; got ruamel.yaml.comments.CommentedMap

Python 3.12.11

The CWL gets validated if in the workflow output the line "secondaryFiles: .bai" get's commented