Passing a quoted string starting with `-` to nextflow CLI has unexpected behaviour

[cjw85]

Bug report

Expected behavior and actual behavior

I would anticipate that passing arguments such as --minimap2_args '-k15' would result in the parameter minimap2_args being set to the string -k15. However, nextflow complains:

Unknown option: -k15 -- Check the available commands and options and syntax with 'help'

Note that the situation is different if the user provides --minimap2_args '-k 15'. The paramater is set to the string -k 15 as expected, so it is not simply that anything starting with '- is taken as an argument for nextflow itself.

Steps to reproduce the problem

nextflow run epi2me-labs/wf-transcriptomes \
        --de_analysis \
        --direct_rna \
        --fastq 'wf-transcriptomes-demo/differential_expression_fastq' \
        --minimap2_index_opts '-k15' \
        --ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \
        --ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \
        --sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
        -profile standard

Program output

Unknown option: -k15 -- Check the available commands and options and syntax with 'help'

There's no nextflow.log produced.

Environment

• Nextflow version: version 24.04.4 build 5917
• Java version: OpenJDK 64-Bit Server VM Temurin-17.0.8.1+1 (build 17.0.8.1+1, mixed mode)
• Operating system: macOS
• Bash version: zsh 5.9 (x86_64-apple-darwin23.0)

Additional context

There's a difference in behaviour compared to when the arguments are provided in a config file as:

params {
        de_analysis = true
        direct_rna = true
        fastq = 'wf-transcriptomes-demo/differential_expression_fastq'
        minimap2_index_opts = '-k15'
        ref_annotation = 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'
        ref_genome = 'wf-transcriptomes-demo/hg38_chr20.fa'
        sample_sheet = 'wf-transcriptomes-demo/sample_sheet.csv'
}

Our users caught this as our documentation contains a CLI invocation built from the contents of the config file, we did not catch it in testing as our CI pipelines run nextflow -c config .... instead.

[bentsherman]

Looks like the underlying CLI library (JCommander) prefers to parse -k15 as a CLI option instead of a parameter value. I believe this problem is solved by #3600 which adds a new CLI based on picocli, but ideally i would want to refactor the existing CLI to also use picocli, which would solve the problem here.

[tamuanand]

Hi @cjw85

As reported by you, I have seen this before err out.

nextflow run epi2me-labs/wf-transcriptomes \
        --de_analysis \
        --direct_rna \
        --fastq 'wf-transcriptomes-demo/differential_expression_fastq' \
        --minimap2_index_opts '-k15' \
        --ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \
        --ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \
        --sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
        -profile standard

However, if you change -k15 to -k 15, it works correctly. So, this below works - would like to know if it works for you

nextflow run epi2me-labs/wf-transcriptomes \
        --de_analysis \
        --direct_rna \
        --fastq 'wf-transcriptomes-demo/differential_expression_fastq' \
        --minimap2_index_opts '-k 15' \
        --ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf' \
        --ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa' \
        --sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv' \
        -profile standard

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