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Description
Expected Behavior
Allow user to specify network access in cwltool:overrides OR explictly error out saying this is not an acceptable override.
Actual Behavior
Tell us what happens instead
We get a warning at the top of the script
overrides.json:3:5: Warning: checking item
overrides.json:4:7: Warning: checking field `requirements`
overrides.json:5:9: Warning: checking item
Warning: Field `class` contains undefined reference to
`file:///home/alexiswl/170612_A00181_0011_AH2JK7DMXX_testing/NetworkAccess`
Input Json
{
"bclconvert_run_configurations": [
{
"strict_mode": false,
"output_directory": "170612_A00181_0011_AH2JK7DMXX_converted",
"samplesheet": {
"bclconvert_data": [
{
"index": "",
"lane": 1,
"sample_id": "PhiX"
}
],
"bclconvert_settings": {
"override_cycles": "Y4N147;Y4N147"
},
"header": {
"application": "NovaSeq FASTQ Only",
"assay": "TruSeq HT",
"chemistry": "Default",
"date": "6/12/2017",
"experiment_name": "170612",
"file_format_version": 2,
"iem_file_version": 4,
"index_adapters": "Truseq",
"instrument_type": "NovaSeq 6000",
"workflow": "GenerateFASTQ"
},
"reads": {
"read_1_cycles": 151,
"read_2_cycles": 151
}
}
}
],
"bclconvert_run_input_directory": {
"class": "Directory",
"location": "170612_A00181_0011_AH2JK7DMXX/"
},
"runfolder_name": "170612_A00181_0011_AH2JK7DMXX",
"cwltool:overrides": {
"workflows/bclconvert/4.0.3/bclconvert__4.0.3.cwl#bcl_convert_run_step": {
"requirements": {
"NetworkAccess": {
"networkAccess": true
}
}
}
}
}Full Traceback
INFO /home/alexiswl/miniconda3/envs/cwltool-latest/bin/cwltool 3.1.20221018083734
INFO Resolved 'bclconvert-with-qc-pipeline__4.0.3/workflow.cwl' to 'file:///home/alexiswl/170612_A00181_0011_AH2JK7DMXX_testing/bclconvert-with-qc-pipeline__4.0.3/workflow.cwl'
input.json:42:5: Warning: checking item
input.json:43:7: Warning: checking field `requirements`
input.json:44:9: Warning: checking item
Warning: Field `class` contains undefined reference to
`file:///home/alexiswl/170612_A00181_0011_AH2JK7DMXX_testing/NetworkAccess`
...Your Environment
- cwltool version:
Check usingcwltool --version
cwltool 3.1.20221018083734
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