Hi there,
I tried the new nextflow module run command, but could not find how to specify “empty input”, any guidelines please ? (a path type in my case)
I tried : "" ; [ ] ; false ; nothing
And value is always resolved as $PWD/value → error because path does not exist
Thanks !
Best,
Felix.
ewels
May 20, 2026, 9:26am
2
Hi @tetedange13 ,
Many thanks for the post - great question! I’m not sure off the top of my head, I think this would be best as a GitHub issue on the Nextflow repo. Are you ok to create one?
Thanks,
Phil
Was about to do it, but when I selected “general question” on Nextflow’s github issues I was redirected here ^^
It is done:
opened 11:34AM - 20 May 26 UTC
lang/modules
## 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
```bash
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
```bash
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](https://github.com/nf-core/modules/blob/master/modules/nf-core/deepvariant/rundeepvariant/main.nf)) :
* `intervals` (from 1st `meta` tuple)
* `tuple val(meta4), path(gzi)`
* `tuple val(meta5), path(par_bed)`
Attached `.module.log` : [module.log.txt](https://github.com/user-attachments/files/28056117/module.log.txt)
Thanks a lot for your quick answer !
Best,
Felix.