cwl-graph-split causes some odd errors for a packed pipeline
alexiswl opened this issue · comments
Steps to reproduce:
mkdir workflow
cwl-graph-split --outdir workflow --output-format yaml --pretty pipeline.cwl.json
Outputs
.
├── fastq-list-row__1.0.0.yaml
├── pipeline.cwl.json
└── workflow
├── custom-touch-file__1.0.0.cwl.cwl
├── dragen-germline__4.2.4.cwl.cwl
├── dragen-somatic__4.2.4.cwl.cwl
├── get-first-non-null-bam-file__1.0.0.cwl.cwl
├── multiqc__1.14.0.cwl.cwl
└── unpacked_pipeline.cwl.json.cwl
I am unsure why the schema fastq-list-row__1.0.0.yaml is placed outside of the workflow directory
I also note that at line 110 of unpacked_pipeline.cwl.json.cwl it seems that the $import truncates the first character of the file to import
- class: "SchemaDefRequirement"
"types":
- "$import": "astq-list-row__1.0.0.yaml"
Should instead be
- class: "SchemaDefRequirement"
"types":
- "$import": "fastq-list-row__1.0.0.yaml"