Using strict syntax causes template to raise an error when setting boolean options on CLI

[scwatts]

When using strict syntax to run a pipeline created by the nf-core/tools template, if a boolean option is defined in the schema with default as false and is then supplied on the CLI, the following error is encountered:

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --my_boolean_option (true): Value is [string] but should be [boolean]

This error only occurs when using Nextflow 25.10.4 with strict syntax enabled or Nextflow 26.02.0-edge (where strict syntax is enabled by default). No error occurs when running via Nextflow 25.10.4 with strict syntax is disabled.

Please see scwatts/nf-core-template-boolean-option-strict-syntax-error for a simple reproducible example.

Also possibly relevant is the nf-core Slack thread

---

Nextflow version: 25.10.4 / 26.02.0-edge
Hardware: MacBook Pro
Executor: local
OS: macOS
nf-core/tools version: 3.5.2 / dev (56f3910)
Python version: 3.11.4

[scwatts]

Also seeing these warnings with the latest template with strict syntax enabled:

WARN: Unrecognized config option 'process.publishDir.path'
WARN: Unrecognized config option 'process.publishDir.mode'
WARN: Unrecognized config option 'process.publishDir.saveAs'
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'

[scwatts]

I've found there are nf-core pipeline releases with strict syntax support that are impacted including nf-core/rnaseq 3.23.0:

$ NXF_VER=25.10.4 NXF_SYNTAX_PARSER=v2 nextflow run nf-core/rnaseq \
  -revision 3.23.0 \
  --gencode \
  --input https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv \
  --outdir output/

 N E X T F L O W   ~  version 25.10.4

Launching `https://github.com/nf-core/rnaseq` [silly_liskov] DSL2 - revision: 13328f7391 [3.23.0]


<<< intervening lines removed, see below for full logfile >>>


ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --gencode (true): Value is [string] but should be [boolean]

Full logged lines (click to show)

 N E X T F L O W   ~  version 25.10.4

Launching `https://github.com/nf-core/rnaseq` [silly_liskov] DSL2 - revision: 13328f7391 [3.23.0]

WARN: Unrecognized config option 'process.publishDir.path'
WARN: Unrecognized config option 'process.publishDir.mode'
WARN: Unrecognized config option 'process.publishDir.saveAs'
WARN: Unrecognized config option 'process.publishDir.enabled'
WARN: Unrecognized config option 'process.publishDir.pattern'
WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq 3.23.0
------------------------------------------------------

Input/output options
  input                                    : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv
  outdir                                   : output/

Reference genome options
  gencode                                  : true

UMI options
  umi_discard_read                         : 0

Generic options
  trace_report_suffix                      : 2026-03-11_15-58-01

Core Nextflow options
  revision                                 : 3.23.0
  runName                                  : silly_liskov
  container..*STAR_ALIGN_IGENOMES          : (dynamic resolved)
  container.STAR_GENOMEGENERATE_IGENOMES   : (dynamic resolved)
  container..*PARABRICKS_STARGENOMEGENERATE: (dynamic resolved)
  launchDir                                : /Users/stephen/projects/temp
  workDir                                  : /Users/stephen/projects/temp/work
  projectDir                               : /Users/stephen/.nextflow/assets/nf-core/rnaseq
  userName                                 : stephen
  profile                                  : standard
  configFiles                              : /Users/stephen/.nextflow/assets/nf-core/rnaseq/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------

* The pipeline
    https://doi.org/10.5281/zenodo.1400710

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
The following invalid input values have been detected:

* --gencode (true): Value is [string] but should be [boolean]

This may mean that boolean options in recent pipeline releases aren't usable when strict syntax is enabled.

[scwatts]

Ben Sherman has provided context here that this is an intentional change:

It is a consequence of the strict syntax and the params block: https://nextflow.io/docs/latest/migrations/25-10.html#deprecations

When strict syntax is enabled, the legacy CLI type casting is disabled, so as to not preempt the params block if you are using it. And strict syntax is now enabled by default on latest edge

I think this then needs to be handled in the nf-schema plugin or in the template

[scwatts]

As far as I understand after discussing further in the linked nextflow-io/nextflow issue the solution for this is to either:

• fully migrate to the new script params block, or alternatively
• use the new script params block to only declare non-string types (e.g. boolean, numerics, etc)

[bentsherman]

Regarding the false warnings:

I think these were fixed in latest edge?

WARN: Unrecognized config option 'process.publishDir.path'
WARN: Unrecognized config option 'process.publishDir.mode'
WARN: Unrecognized config option 'process.publishDir.saveAs'

These should be fixed in nf-schema@2.6.1 or later

WARN: Unrecognized config option 'validation.defaultIgnoreParams'
WARN: Unrecognized config option 'validation.monochromeLogs'

[bentsherman]

As for the issue with boolean options, maybe the nf-schema plugin should be updated to not assume that boolean params have been cast to boolean?

It's a bit of a transitional thing since much of the nf-schema validation will eventually be replaced by the params block. We just need to find a good solution for users in the middle (using strict syntax but still using legacy params)

@nvnieuwk let me know if this thread makes sense to you. I'm happy to work with you to find a sensible fix for nf-schema

[nvnieuwk]

Hi, yeah that should be fairly easily fixable. I can add a custom boolean validator when strict syntax is used. Does this also happen for integers and floats?

Is there a way to easily check which syntax parser is used in plugins?

[bentsherman]

You can use NF.isSyntaxParserV2()

I think the logic is:

• if strict syntax is enabled, you cannot assume that CLI params have been properly converted from a string
• in that case, you should accept strings for booleans / integers / floats as long as they can be parsed as such

You can copy the logic in CmdRun::parseParamValue(), that should essentially restore the legacy behavior but in nf-schema

[nvnieuwk]

Thanks I implemented a fix in this PR: nextflow-io/nf-schema#208