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] 

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] 

(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