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Setting --extra_salmon_quant_args "--noLengthCorrection" leads to the following error message: The following invalid input values have been detected: * --extra_salmon_quant_args: expected type: String, found: Boolean (true)
I believe the reason for this error is that the quotes surrounding --noLengthCorrection are removed somewhere along the way. This is based on there being no quotes around it in the DEBUG nextflow.cli.Launcher line in the log file.
Command used and terminal output
No response
Relevant files
No response
System information
Nextflow version 23.10.0
nf-core/rnaseq 3.14.0
singularity
The text was updated successfully, but these errors were encountered:
I just encountered this issue myself while working on a custom pipeline that uses the same extra_args option as the rnaseq pipeline. From what I can tell, the problem only appears when providing a single extra argument, but it works fine for multiple ones.
For example:
--fastp_extra_args '--trim_poly_x' # interpreted as --trim_poly_x: true at the nextflow level
--fastp_extra_args '--trim_poly_x -y' # both args are interpreted by fastp only
The modules.config entry for the FASTP module contains this line:
params.fastp_extra_args ?: ''
And the parameter was also made available in the nextflow.config file.
Single and double quotes appear to behave similarly.
All of the above applies to the CLI, I did not test the behaviour when using a params.yml file.
Description of the bug
Setting --extra_salmon_quant_args "--noLengthCorrection" leads to the following error message:
The following invalid input values have been detected: * --extra_salmon_quant_args: expected type: String, found: Boolean (true)
I believe the reason for this error is that the quotes surrounding --noLengthCorrection are removed somewhere along the way. This is based on there being no quotes around it in the
DEBUG nextflow.cli.Launcher
line in the log file.Command used and terminal output
No response
Relevant files
No response
System information
Nextflow version 23.10.0
nf-core/rnaseq 3.14.0
singularity
The text was updated successfully, but these errors were encountered: