Workflow 'publish:' feature and optional processes

[maressyl]

Hi,

I'm experimenting with this very promising feature of defining files to publish directly in the workflow, however I can't figure out how to deal with my optional processes (processes which run only if a specific params boolean is set). Here is a simplified example of my current pipeline :

workflow {

	... many processes ...

	if(params.varcall) {
		
		... many processes ...

		mutect2(...)
	}
	
	publish:
	bam_sort.out.BAM >> 'BAM'
	edgeR.out.TSV >> 'expression'
	multiqc.out.HTML >> 'QC'
	mutect2.out.VCF >> 'variants'
}

output {
	directory { params.output }
	
	'variants' {
		enable false
		ignoreErrors true
	}
}

The documentation suggests numerous ways of disabling publication (enable false, ch_foo >> (params.save_foo ? 'foo' : null)...) or ignoring errors during publications, but whatever I use I still get the following error, which seems to be triggered before all these mechanisms fire :

N E X T F L O W  ~  version 24.04.4
WARN: It appears you have never run this project before -- Option `-resume` is ignored
Launching `/srv/scratch/DEPOT/pipelines/SAMI-V2/main.nf` [awesome_leakey] DSL2 - revision: 31b9236abf
WARN: WORKFLOW OUTPUT DSL IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
Access to 'mutect2.out' is undefined since the process 'mutect2' has not been invoked before accessing the output attribute

 -- Check script '/srv/scratch/DEPOT/pipelines/SAMI-V2/main.nf' at line: 477 or see '.nextflow.log' file for more details

Did I miss something ?

Best regards,
Sylvain

[bentsherman]

For conditional processes, you can't rely on the .out property in the publish section because that property won't exist when the process isn't invoked. You have to do something like this:

workflow {

	if (params.varcall) {
		mutect2(...)
                vcf = mutect2.out.VCF
	}
        else {
                vcf = Channel.empty()
        }
	
	publish:
	vcf >> 'variants'
}