Update debug lesson for fruitfly examples

[douglowe]

Instructions

Thanks for contributing! :heart: Keep in mind that **lesson maintainers are volunteers** and it may take them some time to respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum. If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact the CWL Team via https://www.commonwl.org/#Support. You may delete these instructions from your comment.

[netlify[bot]]

✅ Add Deploy Preview notifications as pull request comments when Deploy Preview succeeds

Name	Link
🔨 Latest commit	def94059243d5f59f1a6b1e0115cc53ae1ad8bdb
🔍 Latest deploy log	https://app.netlify.com/sites/thirsty-hoover-1e0704/deploys/62bb3c6add8892000993aca5
😎 Deploy Preview	https://deploy-preview-121--thirsty-hoover-1e0704.netlify.app
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

---

To edit notification comments on pull requests, go to your Netlify site settings.

[mr-c]

Execution results with new line numbers:

$ cwltool rna_seq_workflow_fieldname_fail.cwl workflow_input_debug.yml 
INFO /home/michael/src/2022-06-28-n8-cwl/env/bin/cwltool 3.1.20220628145801
INFO Resolved 'rna_seq_workflow_fieldname_fail.cwl' to 'file:///home/michael/src/2022-06-28-n8-cwl/novice-tutorial-exercises/rna_seq_workflow_fieldname_fail.cwl'
ERROR Tool definition failed validation:
rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
                                          because
                                            tried `Workflow` but
rna_seq_workflow_fieldname_fail.cwl:35:1:     the `outputs` field is not valid because
rna_seq_workflow_fieldname_fail.cwl:36:3:       item is invalid because
rna_seq_workflow_fieldname_fail.cwl:38:5:         invalid field `outputsource`, expected one of:
                                                  'label', 'secondaryFiles', 'streamable', 'doc', 'id',
                                                  'format', 'outputSource', 'linkMerge', 'pickValue', 'type'

$ cwltool rna_seq_workflow_varname_fail.cwl workflow_input_debug.yml 
INFO /home/michael/src/2022-06-28-n8-cwl/env/bin/cwltool 3.1.20220628145801
INFO Resolved 'rna_seq_workflow_varname_fail.cwl' to 'file:///home/michael/src/2022-06-28-n8-cwl/novice-tutorial-exercises/rna_seq_workflow_varname_fail.cwl'
ERROR Tool definition failed validation:
rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
rna_seq_workflow_varname_fail.cwl:29:3:   checking object
                                          `rna_seq_workflow_varname_fail.cwl#index_alignment`
rna_seq_workflow_varname_fail.cwl:31:5:     checking field `in`
rna_seq_workflow_varname_fail.cwl:32:7:       checking object
                                              `rna_seq_workflow_varname_fail.cwl#index_alignment/bam_sorted`
                                                Field `source` references unknown identifier
                                                `mapping_reads/alignments`, tried
                                                file:///home/michael/src/2022-06-28-n8-cwl/novice-tutorial-exercises/rna_seq_workflow_varname_fail.cwl#mapping_reads/alignments

$ cwltool rna_seq_workflow_type_fail.cwl workflow_input_debug.yml
INFO /home/michael/src/2022-06-28-n8-cwl/env/bin/cwltool 3.1.20220628145801
INFO Resolved 'rna_seq_workflow_type_fail.cwl' to 'file:///home/michael/src/2022-06-28-n8-cwl/novice-tutorial-exercises/rna_seq_workflow_type_fail.cwl'
WARNING Workflow checker warning:
rna_seq_workflow_type_fail.cwl:27:11: Source 'alignment' of type ["File", {"type": "array",
                                      "items": "File"}] may be incompatible
rna_seq_workflow_type_fail.cwl:32:7:    with sink 'bam_sorted' of type "File"
ERROR Tool definition failed validation:

rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
rna_seq_workflow_type_fail.cwl:23:7:   with sink 'ForwardReads' of type ["File", {"type":
                                       "array", "items": "File"}]

ERROR Exception on step 'mapping_reads'
ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format https://edamontology.org/format_1930 but
  File has no 'format' defined: {
    "class": "File",
    "location": "file:///home/michael/src/2022-06-28-n8-cwl/novice-tutorial-exercises/rnaseq/GSM461177_1_subsampled.fastqsanger",
    "size": 142867948,
    "basename": "GSM461177_1_subsampled.fastqsanger",
    "nameroot": "GSM461177_1_subsampled",
    "nameext": ".fastqsanger"
}