cwl-graph-split causes some odd errors for a packed pipeline

[alexiswl]

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"

Inputs Zip

pipeline.zip

Outputs zip

graph_split.zip