declared and specified channels

[zaidissa]

I am building a nf pipeline that performs CNV calling in nextflow. In my mind I am correctly declaring all input channels but I still keep getting error of "Process test_CNV:SCEVAN declares 3 input channels but 4 were specified"
I am sharing the files, I would really appreciate if I can get some guidance/help

main.nf

include { test_CNV } from './subworkflow/local/test_CNV.nf'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Check mandatory parameters
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

if (params.input_seurat_object)   { input_seurat_object = file(params.input_seurat_object) } else { exit 1, 'Please, provide a --input_seurat_object <PATH/TO/seurat_object.RDS> !' }
if (params.input_reference_table) { input_reference_table = file(params.input_reference_table) } else { exit 1, 'Please, provide a --input_reference_table <PATH/TO/seurat_object.RDS> !' }

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    RUN ALL WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

    log.info """\

        Parameters:

        Input: ${input_seurat_object}
        Reference cells: ${input_reference_table}

    """

    // Mandatory inputs
    ch_seurat_object    = Channel.fromPath(params.input_seurat_object, checkIfExists: true)

    // Optional inputs
    ch_reference_table  = Channel.fromPath(params.input_reference_table, checkIfExists: true)

    // Running subworkflows
    yest_CNV(
        ch_seurat_object,
        ch_reference_table
    )

}

subworkflow/local/test_CNV.nf

#!/usr/bin/env nextflow

include {  INFERCNV     } from '../../modules/local/infercnv/main.nf'
include {  SCEVAN       } from '../../modules/local/scevan/main.nf'
include { COPYKAT } from '../../modules/local/copykat/main.nf' // Re-added from your first shared code for completeness


workflow test_CNV {

    take:
        ch_seurat_object     // channel: []
        ch_reference_table   // channel: []

    main:

        // Importing notebook
        ch_notebook_infercnv  = Channel.fromPath(params.notebook_infercnv, checkIfExists: true)
        ch_notebook_scevan    = Channel.fromPath(params.notebook_scevan, checkIfExists: true) // Use params.notebook_scevan
        ch_notebook_copykat = Channel.fromPath(params.notebook_copykat, checkIfExists: true) // Re-added for completeness


        // Quarto configurations
        ch_template    = Channel.fromPath(params.template, checkIfExists: true)
            .collect()
        ch_page_config = Channel.fromPath(params.page_config, checkIfExists: true)
            .collect()


        // Version channel
        ch_versions = Channel.empty()

        // Passing notebooks for respective functions
        // Run inferCNV
        if (!params.skip_infercnv) { // Added 'if' conditions back from previous versions for robustness
            INFERCNV(
                ch_seurat_object,
                ch_reference_table,
                ch_notebook_infercnv,
                ch_page_config // Pass the *original*, simple ch_page_config
            )
        }

        // Run SCEVAN
        if (!params.skip_scevan) {
            SCEVAN(
                ch_seurat_object,
                ch_notebook_scevan,
                ch_page_config // Pass the *original*, simple ch_page_config
            ) { // Keep the ext.args block if it's intended to be there for SCEVAN
                ext.args = """
                    project_name=${params.project_name}
                    input_model=${params.organism}
                    n_threads=${params.max_cpus}
                    n_memory=${params.max_memory}
                    workdir=${params.outdir}/${params.project_name}
                    auto_save=true
                """
            }
        }



    emit:
        versions = ch_versions

}

[bentsherman]

What are you trying to do with the curly braces after the process call? It is treated as a fourth argument, as if you had written this:

            SCEVAN(
                ch_seurat_object,
                ch_notebook_scevan,
                ch_page_config,
                {
                  ext.args = // ...
                }
            )

[zaidissa]

do you think this could cause the error "Process test_CNV:SCEVAN declares 4 input channels but 3 were specified"?

[zaidissa]

I have it in the config file and removed from here

[bentsherman]

yes, when you had it in the code it was being interpreted as a fourth input channel instead of configuration

[zaidissa]

let me try that.

[zaidissa]

worked. Thanks, somehow, I was overlooking this

Appreciated