search

umccr / icav2-cli-plugins

A set of additional subcommands for icav2
MIT License
2 stars 0 forks source link

ProjectPipelines create-wes-template provides incorrect examples for cwltool overrides #275

Open alexiswl opened 1 month ago

alexiswl commented 1 month ago

Gives run_dragen_somatic_step instead of workflow.cwl#dragen-somatic-with-germline-pipeline--4.2.4/run_dragen_somatic_step

alexiswl commented 1 month ago

Related to https://github.com/common-workflow-language/cwltool/issues/1754, should instead have a note to say what the override should be given the cwltool version

alexiswl commented 1 month ago

Infact to override requirements for a tool, one should use tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.cwl#dragen-somatic--4.2.4 instead, since tool requirements will take precedence over the workflow step requirements.