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The new-ish positional args warning in nf-core pipelines has some misleading behaviour in at least one edge-case.
Using -stub-run/-stub will produce the following:
WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected.
Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`.
It seems that nextflow sets -stub to have a value of "true" when it normalises args which for whatever reason is later treated as an unattached positional arg?
This might be both an nf-core issue in that the check is rathe blunt, but also a nextflow issue because it seems weird to inject a normalised arg value into the positional args?
Command used and terminal output
No response
System information
nextflow 23.10.1
The text was updated successfully, but these errors were encountered:
Description of the bug
The new-ish positional args warning in nf-core pipelines has some misleading behaviour in at least one edge-case.
Using
-stub-run
/-stub
will produce the following:It seems that
nextflow
sets-stub
to have a value of"true"
when it normalises args which for whatever reason is later treated as an unattached positional arg?This might be both an
nf-core
issue in that the check is rathe blunt, but also anextflow
issue because it seems weird to inject a normalised arg value into the positional args?Command used and terminal output
No response
System information
nextflow 23.10.1
The text was updated successfully, but these errors were encountered: