Missing output paramater ERROR when using nextflow v.25. Works fine on previous versions

[marcellobeltrami]

Missing workflow output parameter: abundances_collection

The whole pipeline has been working so far. I tried to update to nf v.25 due to better error messages, but the pipeline is now broken. I tried to fix it by changing variables, collecting files in different ways, setting preview to false but to no availI am not too sure if this is my own doing or perhaps a bug?

Thank you to anyone that can help :)

Running PairedAlignWK workflow
[-        ] PairedAlignWK:TrimmingPaired            -
[-        ] PairedAlignWK:FastQC                    -
[-        ] PairedAlignWK:KallistoPaired            -
[-        ] PairedAlignWK:MultiQC                   -
[-        ] PairedAlignWK:RemoveTranscriptsVersions -
Missing workflow output parameter: abundances_collection

main

workflow {
    
    // Checks input structures, file existance, etc..
    if (params.check_inputs == true){
        CheckInputs()
    }
    
    if (params.PE == true) {
        reads_channel = Channel
            .fromPath(params.reads)
            .splitCsv(header: false, skip: 1, sep: ',')
            .map { row -> tuple(row[0], row[1], row[2]) }
        
        quantized = PairedAlignWK(reads_channel) // WORKFLOW CALLED HERE
    } else {
        reads_channel = Channel
            .fromPath(params.reads)
            .splitCsv(header: false, skip: 1, sep: ',')
            .map { row -> tuple(row[0], row[1]) }
        
        quantized = UnpairedAlignWK(reads_channel)
    }

    if (params.t2g == false && params.DE == true) {
        SleuthTranscriptsWK(quantized.abundances_collection, quantized.merged_TPMs)
    } else if (params.t2g != false && params.DE == true) {
        SleuthT2GWK(quantized.abundances_collection, quantized.merged_TPMs)
    } else if (params.DE == false) {
        log.info "DE set to false, skipping differential expression analysis" 
    }

}

workflow

workflow PairedAlignWK{ 

    take:
        reads_channel

    main: 

        // Carries out trimming if required.
        if (params.trim) {
            trimmed = TrimmingPaired(reads_channel)
            trimmed_tuple = trimmed.trimmed_tuple
        }
        else {
            trimmed_tuple = reads_channel
        }

        // Collects the metrics from FastQC and Kallisto and compiles them in a single MultiQC report
        qc = FastQC(trimmed_tuple)  
        abundance_files = KallistoPaired(trimmed_tuple)
        ch_multiqc_files = Channel.empty()
        ch_multiqc_files = ch_multiqc_files.mix(qc.results.collect())
        ch_multiqc_files = ch_multiqc_files.mix(abundance_files.metrics.collect())

        MultiQC(ch_multiqc_files.collect())

        // Removes unwanted transcripts and transcript versions
        if (params.unwanted_transcripts == true){
            unwanted_dir = RemoveUnwanted(abundance_files.directory, params.unwanted_transcripts).filtered_tuple
        } else { 
            unwanted_dir = abundance_files.directory
        }
        
        transc_version_rm = RemoveTranscriptsVersions(unwanted_dir)
        transc_exp = transc_version_rm.filtered_tuple
        
        // Optionally remove gencode annotation
        if (params.gencode) {
            gencode_format = GencodeFormat(transc_version_rm.filtered_tuple)
            transc_exp = gencode_format.gencoded_tuple
        } else {
            transc_exp = transc_version_rm.filtered_tuple
        }
    
        // Prepare channels for tximport and output
        kallisto_paths = transc_exp.flatMap { _sample_id, path -> [path] }
        kallisto_dir_collection = kallisto_paths.toList()  // For tximport input
        abundances_for_output = kallisto_paths.collect()   // For workflow output

        // Carries tximport and produces merged dataframe.
        if (params.t2g) {   
            tximport_TPMs = TXimportT2G(kallisto_dir_collection)
        } else {
            tximport_TPMs = TXimportTranscripts(kallisto_dir_collection)
        }

    emit:
        abundances_collection = abundances_for_output // channel emitting complete kallisto output directory
        merged_TPMs = tximport_TPMs.merged_TPM // merged TPM dataframe
}

[bentsherman]

I think this is a bug with the new parser that is fixed in the latest patch release. Try it with 25.04.4

[marcellobeltrami]

Hi Ben,

Thank you, it was a bug with the new parser. Have a lovely day :).