Often that error is actually the fault of an invalid (too long/short) input tuple

Sorry, I wasnt precise before, thats an issue when using

NXF_VER=26.04.6 nextflow config -o json

. With that info, is that still a potential issue with the input tuble? Because the pipeline itself runs fine (

nextflow run ampliseq -profile test --outdir results

).

Oh, that's different. Do you have a config variable where something accessing

task

is not wrapped in a closure?

Hm, something like

ext.args = '--p-prv-cut 0.1 --p-lib-cut 500 --p-alpha 0.05 --p-conserve'
ext.prefix = { meta.region ? "region-${meta.region}_run-${meta.run}" : "${meta.run}" }
ext.quality_type = { "${params.quality_type}" }

where the first isnt in a closure, is that needed now?

It's only needed if the result needs to access

task

,

meta

, etc.

Hm no I cannot find any

task.

outside of a closure. The AI also says that for modules.config "In all cases

task.process

sits inside a

{ ... }

closure bound to the

path:

key." & base.config "confirming

task.

only appears where a closure is used."...

Interesting!

Each one of those three cause the issue it seems:

withName: 'GAPPA_GRAFT' {
        ext.prefix = { "${meta.id}.graft" }
        publishDir = [
            [
                path: { "${params.outdir}/pplace" },
                mode: params.publish_dir_mode,
                pattern: "*.newick"
            ],
            [
                path: { "${params.outdir}/pplace/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
                mode: params.publish_dir_mode,
                saveAs: { filename -> filename ? (filename == 'versions.yml' ? null : filename) : null }
            ]
        ]
    }

    withName: 'GAPPA_ASSIGN' {
        ext.prefix = { "${meta.id}.taxonomy" }
        ext.args   = "--per-query-results --krona --sativa"
        ext.when   = { taxonomy }
        publishDir = [
            [
                path: { "${params.outdir}/pplace" },
                mode: params.publish_dir_mode,
                pattern: "*.taxonomy.per_query.tsv"
            ],
            [
                path: { "${params.outdir}/pplace/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
                mode: params.publish_dir_mode,
                saveAs: { filename -> filename ? (filename == 'versions.yml' ? null : filename) : null }
            ]
        ]
    }

    withName: 'GAPPA_HEATTREE' {
        ext.prefix = { "${meta.id}.heattree" }
        ext.args = "--write-nexus-tree --write-phyloxml-tree --write-svg-tree"
        publishDir = [
            [
                path: { "${params.outdir}/pplace" },
                mode: params.publish_dir_mode,
                pattern: "*.tree.svg"
            ],
            [
                path: { "${params.outdir}/pplace/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
                mode: params.publish_dir_mode,
                saveAs: { filename -> filename ? (filename == 'versions.yml' ? null : filename) : null }
            ]
        ]
    }

investigating...

you need to escape the task

Thanks so far, a lot! Will continue that after lunch 😄

Alternatively you don't fix any of this and wait for 26.04.7 to be released with the fix, and merge PRs with manual linting with a working version

Thanks again, was not too bad after all: https://github.com/nf-core/ampliseq/pull/1077/changes/c1bcf5f559356448f907769d99ed36469486f4d6