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nf-core
comparison of default values returns unclear error
Description of the bug
Just run nf-core schema build to edit some arguments. However, some arguments were flagged as not matching, although they looked perfectly identical! The underlying issue was that the argument types were not matching. But I had to dig a bit here.
Command used and terminal output
nf-core schema build
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.13 - https://nf-co.re
INFO [✓] Default parameters match schema validation
INFO [✓] Pipeline schema looks valid (found 66 params)
✨ Default for 'params.wfmash_segment_length' in the pipeline config does not match schema. (schema: '5000' | config: '5000'). Update pipeline schema? [y/n]: n
✨ Default for 'params.wfmash_sparse_map' in the pipeline config does not match schema. (schema: '1.0' | config: '1'). Update pipeline schema? [y/n]: n
✨ Default for 'params.seqwish_transclose_batch' in the pipeline config does not match schema. (schema: '10000000' | config: '10000000'). Update pipeline schema? [y/n]: n
✨ Default for 'params.validationLenientMode' is not in schema (def='True'). Update pipeline schema? [y/n]: n
INFO Writing schema with 66 params: 'nextflow_schema.json'
🚀 Launch web builder for customisation and editing? [y/n]: y
INFO Opening URL: https://nf-co.re/pipeline_schema_builder?id=1708683972_a55402ad9c18
INFO Waiting for form to be completed in the browser. Remember to click Finished when you're done.
⣷ Use ctrl+c to stop waiting and force exit.INFO Found saved status from nf-core schema builder
INFO Writing schema with 66 params: 'nextflow_schema.json'
⣟ Use ctrl+c to stop waiting and force exit.
System information
nf-core version 2.13.
Should the types not be the same? If a parameter is meant to be an int and the default is set as a str (I assume that's what happens here) is that not wrong?
