When MaheshForm is selected in settings the extension then highlights the entire process in red after applying Format Document.

[mahesh-panchal]

When using MaheshForm from the settings, the extension highlights the entire process in red after using Format Document.

[bentsherman]

Can you provide a minimal example?

[mahesh-panchal]

Before, no issue:

process FILTER_FIVE_END {
    tag "$meta.id"
    label 'process_medium'

    container "community.wave.seqera.io/library/samtools_perl:e2ce3f7265547d1f"

    input:
    tuple val(meta), path(bam)

    output:
    tuple val(meta), path("*.bam")  , emit: bam
    path "versions.yml"             , emit: versions

    when:
    task.ext.when == null || task.ext.when

    script:
    def prefix = task.ext.prefix ?: "${meta.id}"

    """
    samtools view -h -@ $task.cpus ${bam} | \\
    filter_five_end.pl | \\
    samtools view -@ $task.cpus -Sb - > ${prefix}.bam

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(samtools --version | sed '1!d; s/.* //')
    END_VERSIONS
    """
}

and then select format document:

after, everything underlined red:

process FILTER_FIVE_END {
    tag "${meta.id}"
    label 'process_medium'

    container "community.wave.seqera.io/library/samtools_perl:e2ce3f7265547d1f"

    input:
    tuple val(meta), path(bam)

    when:
    task.ext.when == null || task.ext.when

    script:
    def prefix = task.ext.prefix ?: "${meta.id}"

    """
    samtools view -h -@ ${task.cpus} ${bam} | \\
    filter_five_end.pl | \\
    samtools view -@ ${task.cpus} -Sb - > ${prefix}.bam

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        samtools: \$(samtools --version | sed '1!d; s/.* //')
    END_VERSIONS
    """

    output:
    tuple val(meta), path("*.bam"), emit: bam
    path "versions.yml", emit: versions
}

with the message: Invalid process definition, check for out-of-order section labels.

[bentsherman]

Whoops, I forgot to include the when: section in the mahesh form. I'll get that fixed, just keep in mind that it might be a while before it gets into the language server, since the parser is now in Nextflow itself.