"nextflow module run" with multiple optional path inputs ?

[tetedange13]

Bug report

Cannot find how to specify (multiple) optional path input with nextflow module run

Expected behavior and actual behavior

I do not know exactly which is the "expected" behaviour here, but actual is impossibilty to run a module with multiple optional path inputs

Steps to reproduce the problem

nextflow-26.04.1-dist module run -with-singularity nf-core/deepvariant/rundeepvariant \
    --meta.id test \
    --input https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam \
    --index https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai \
    --intervals "" \
    --meta2.id fasta \
    --fasta https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta \
    --meta3.id fai \
    --fai https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai \
    --meta4.id gzi \
    --gzi "" \
    --meta5.id par \
    --par_bed "" \
    --outdir test_out

And dv.config containing

process {
  withName: DEEPVARIANT_RUNDEEPVARIANT {
    ext.args = "--model_type WGS"
  }
}

Program output

Multiple possible errors depending on what I tried :

• All optional inputs to <empty_string> or <empty_list> -> input file name collision
• Put different fake filenames (not existing) -> tool error when it tries to handle non-existing file
• Excluding optional inputs from command-line -> Missing required parameter

Environment

• Nextflow version: 26.04.1
• Java version: openjdk 23.0.2-internal 2025-01-21
• Operating system: Linux
• Bash version: GNU bash, version 5.2.37(1)-release (x86_64-pc-linux-gnu)

Additional context

In above command, multiple path inputs are optional, these are for sure (based on module code) :

• intervals (from 1st meta tuple)
• tuple val(meta4), path(gzi)
• tuple val(meta5), path(par_bed)

Attached .module.log : module.log.txt

[bentsherman]

I think we can resolve this by interpreting an empty string as [], since that is the only way to pass an optional file input for legacy processes

I will see if we can also make it work by not specifying the option at all. Just need to see if we can do it without degrading the error messages for required inputs