(base) [hoge@gc129 VIRTUS]$ cwltool --singularity workflow/createindex.cwl workflow/createindex.job.yaml --debug
INFO /home/hoge/anaconda3/bin/cwltool 3.1.20210426140515
INFO Resolved 'workflow/createindex.cwl' to 'file:///share/home/hoge/VIRTUS/workflow/createindex.cwl'
workflow/createindex.cwl:39:5: object id `workflow/createindex.cwl#createindex/salmon_index_human` previously defined
workflow/createindex.cwl:39:5: object id `workflow/createindex.cwl#createindex/salmon_index_human` previously defined
workflow/createindex.cwl:148:9: object id `workflow/createindex.cwl#createindex/salmon_index_human/index` previously defined
tool/salmon-cwl/salmon-index.cwl:8:5: object id `tool/salmon-cwl/salmon-index.cwl#index` previously defined
usage: workflow/createindex.cwl [-h] --url_virus URL_VIRUS --output_name_virus
                                OUTPUT_NAME_VIRUS [--runThreadN RUNTHREADN]
                                --dir_name_STAR_virus DIR_NAME_STAR_VIRUS
                                --url_genomefasta_human URL_GENOMEFASTA_HUMAN
                                --output_name_genomefasta_human
                                OUTPUT_NAME_GENOMEFASTA_HUMAN
                                --dir_name_STAR_human DIR_NAME_STAR_HUMAN
                                --salmon_index_human SALMON_INDEX_HUMAN
                                --url_transcript_human URL_TRANSCRIPT_HUMAN
                                --output_name_human_transcipt
                                OUTPUT_NAME_HUMAN_TRANSCIPT
                                [job_order]
workflow/createindex.cwl: error: the following arguments are required: --url_virus, --output_name_virus, --dir_name_STAR_virus, --url_genomefasta_human, --output_name_genomefasta_human, --dir_name_STAR_human, --salmon_index_human, --url_transcript_human, --output_name_human_transcipt