Comment formatting and deletion upon saving

[arptier]

Hello!

Similar to this issue which was previously reported and resolved, upon saving my file, in-line comments to the right of scripts are moved below the line to which they reference. For example,

params.index_ref = null     // Path to index reference genome

becomes

params.index_ref = null
// Path to index reference genome

Additionally, if the last line of the workflow is commented out, upon saving, that line and all other commented lines below the bottommost uncommented line will be deleted. So for example,

workflow {
    
    fastq_files_ch = Channel.fromFilePairs(params.fastq_inputs)
    fastq_files_ch.view()

    // PROCESS_1(fastq_files_ch)
    // new_ch = PROCESS_1.out
    // PROCESS_2(new_ch)
}

after saving, becomes:

workflow {
    
    fastq_files_ch = Channel.fromFilePairs(params.fastq_inputs)
    fastq_files_ch.view()

}

I am using the Nextflow language support extension Version 1.5.0 released 17 Jun 2025.

My user settings are:

    "files.trimTrailingWhitespace": false,
    "nextflow.debug": true,
    "nextflow.completion.extended": true,
    "nextflow.formatting.harshilAlignment": true

I have tried toggling each of these settings and they do not appear to stop the commented lines from disappearing on saving.

Thank you!

[hy911]

I have the same problem. Have you solved yours?

[arptier]

I have the same problem. Have you solved yours?

Unfortunately, not. I just work around it. I imagine this bug may be something they address in a later version.

[TheLostLambda]

I've also run into this issue — I was quite perplexed when my comments were getting deleted automatically!

I went from this:

params.ldt_domains = [
    'IPR005490', // YkuD
    'IPR007391', // VanW
]

To this, when I saved the file and format was run!

params.ldt_domains = [
    'IPR005490',
    'IPR007391',
]