As mentioned in issue: https://github.com/common-workflow-language/cwltool/pull/507
cwltool allows http/https as input, that means it will automatically download and stage the remote input files for both tools and workflows.
One question here is: does cwltool also support the secondaryFiles which are also remote?
If define workflow.cwl file as:
Inputs: ref_file: type: File? secondaryFiles: ['.fai?']
Can I define the input in the job.yaml file as following:
ref_file: path: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa class: File secondaryFiles: - class: File path: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai