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parameter normalization regression remains in params-file declarations #5987

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yttria-aniseia opened this issue Apr 19, 2025 · 0 comments · Fixed by #5989
Closed

parameter normalization regression remains in params-file declarations #5987

yttria-aniseia opened this issue Apr 19, 2025 · 0 comments · Fixed by #5989
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Bug report

#5661 doesn't fix kebab-case parameters specified in -params-file.

Expected behavior and actual behavior

regression described in #5655 applies to declarations in params-file, which, per documentation, should be equivalent to parameters passed in cli.

Parameters defined in the file are equivalent to specifying them directly on the command line

Steps to reproduce the problem

test.nf:

params.longParam = "unchanged"

workflow {
        log.info "${params}"
        log.info "${params.longParam}"
}

test.yaml:

long-param: kebab

test2.yaml:

longParam: camel

Program output

23.10.1

# nextflow run test.nf --long-param kebab
[long-param:kebab, longParam:kebab]
kebab
# nextflow run test.nf --longParam camel
[longParam:camel, long-param:camel]
camel
# nextflow run test.nf -params-file test.yaml
[long-param:kebab, longParam:kebab]
kebab
# nextflow run test.nf -params-file test2.yaml
[longParam:camel, long-param:camel]
camel

24.10.5

# nextflow run test.nf --long-param kebab
[longParam:kebab]
kebab
# nextflow run test.nf --longParam camel
[longParam:camel]
camel
# nextflow run test.nf -params-file test.yaml
[long-param:kebab, longParam:unchanged]
unchanged
# nextflow run test.nf -params-file test2.yaml
[longParam:camel]
camel

Environment

  • Nextflow version: 24.10.5
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Fix kebab-case normalization for params file nextflow-io/nextflow
2 participants
@bentsherman @yttria-aniseia