Inconsistent behaviour with aliased process names and aliased workflows in process selectors #6682
Description
Bug report
Expected behavior and actual behavior
Aliased processes are able to be selected in config using their "true" (base? original?) name. This is very useful when trying to set config that should be the same across all aliased processes of given process.
However this does not work if anything other than the process name is used (i.e. fully qualified name) in the selector.
And it does not work for aliased subworkflows.
The working case
Consider the following workflow:
module.nf
process A_A {
output:
val("${task.ext.args}"), emit: val
script:
"""
echo ${task.ext.args}
"""
}
main.nf
include { A_A; A_A as A_B } from './module.nf'
workflow PARENT {
A_A()
A_A.out.val.view{ it -> "A: ${it}" }
A_B()
A_B.out.val.view{ it -> "B: ${it}" }
}
workflow {
PARENT()
}
Given the following config:
process {
withName: "A_B" {
ext.args = 'b'
}
withName: "A_A" {
ext.args = 'a'
}
}
OUTPUT
B: b
A: a
Given:
process {
withName: "A_A" {
ext.args = 'a'
}
}
OUTPUT
B: a
A: a
Aliased Process with subworkflow selector
Given:
process {
withName: "PARENT:A_B" {
ext.args = 'b'
}
withName: "PARENT:A_A" {
ext.args = 'a'
}
}
OUTPUT
B: b
A: a
But given:
process {
withName: "PARENT:A_A" {
ext.args = 'a'
}
}
OUTPUT
B: null
A: a
Aliased subworkflow
main.nf
include { PARENT; PARENT as PARENT2 } from './subwf.nf'
workflow {
PARENT()
PARENT2()
}
Given:
process {
withName: "A_B" {
ext.args = 'b'
}
withName: "A_A" {
ext.args = 'a'
}
}
OUTPUT
B: b
B: b
A: a
A: a
Given:
process {
withName: "PARENT:A_B" {
ext.args = 'b'
}
withName: "PARENT:A_A" {
ext.args = 'a'
}
}
OUTPUT
A: a
B: null
A: null
B: b
Environment
- Nextflow version: 25.10.2