Subworkflow alias not being recognized in module.config

[bielasilva]

Hi. I have been facing an issue and I am not sure if it's indeed a bug, or just not how Nextflow operates.

Since Nextflow cannot reuse the same subworkflow, I have imported it multiple times.

include { RACON_POLISHER as RACON_POLISHER1 } from './polishing/racon_polisher'
include { RACON_POLISHER as RACON_POLISHER2 } from './polishing/racon_polisher'

if ( params.polishIterations >= 1 ) {
    RACON_POLISHER1( ch_reads, ch_polish )
    ch_polish = RACON_POLISHER1.out.genome
}
 if ( params.polishIterations >= 2 ) {
    RACON_POLISHER2( ch_reads, ch_polish )
    ch_polish = RACON_POLISHER2.out.genome
} 

This works, however, since the intake file for RACON_POLISHER2 has the output name, it's marked as already existing when that process finishes

gzip: ${prefix}_assembly_consensus.fasta.gz already exists;     not overwritten

To solve that, I have tried to make the prefix different for each run in the modules.config file. But it's failing to recognize each call and change the prefix.

process {
withName: 'RACON_POLISHER1:RACON' {
        ext.prefix = { "${meta.id}_polisher1" }
    }

    withName: 'RACON_POLISHER2:RACON' {
        ext.prefix = { "${meta.id}_polisher2" }
    }
}

When I just specify the RACON module, it does change, but then again, I can't reuse the file as it has the same name for all RACON runs.

process {
withName: 'RACON' {
        ext.prefix = { "${meta.id}_polisher1" }
    }
}

Shouldn't SUBWORKFLOW:PROCESS be recognized and change the parameters for the PROCESS call?

Environment

• Nextflow version: 24.10.3
• Java version: openjdk 21.0.5 2024-10-15 LTS
• Operating system: CentOS Linux 7
• Bash version: zsh 5.9 (x86_64-pc-linux-gnu)