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Sub-workflow is not inheriting replaced param values #4982
Comments
The params map is intended to be immutable, likely this |
I see things like this in nf-core pipelines where params are overwritten (I think). |
We are moving away from that pattern. Those params should really just be variables |
It would be great to have this be documented somewhere so we don’t have the rug pulled out from us for patterns that are in use today. |
We are developing some clearer and stricter guidance on what is allowed in the DSL, since the Groovy compiler allows way more than what is intended for Nextflow. We're still working out some details, but we will definitely provide documentation (and tooling 😄 ) once it's ready. |
Bug report
Expected behavior and actual behavior
When calling
.replace
on theparams
object inmain.nf
, I would expect that any access to theparams
object in any workflow or sub-workflow would return the updated copy. This is not the case.Steps to reproduce the problem
main.nf
params.yml
sub_main.nf
Program output
Notice how
SUB_MAIN::params
prints out[foo:bar]
, not the expected[foo:bar-has-been-replaced]
.Environment
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