Fastq columns in nf-core pipeline even though they are not part of the samplesheet

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1

I created a pipeline using the nf-core framework. I got a strange error that happened at the sample sheet level, my samplesheet has five columns:

sample,bam,bai,vcf,tbi
(notice no fastq anywhere)

and as I was digging in I saw the following on subworkflows/local/utils_nfcore_my_pipeline:

//
// Create channel from input file provided through params.input
//

    Channel
        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
        .map {
            meta, fastq_1, fastq_2 ->
                if (!fastq_2) {
                    return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ]
                } else {
                    return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ]
                }
        }
        .groupTuple()
        .map { samplesheet ->
            validateInputSamplesheet(samplesheet)
        }
        .map {
            meta, fastqs ->
                return [ meta, fastqs.flatten() ]
        }
        .set { ch_samplesheet }

Which referes to fastqs ,etc. It seems that I need to edit this file?

2

For anybody seeing this, it was answered on slack by @Alexander_Nater: " Alexander NaterAlexander Nater Today at 1:01 PM

Yes, you need to edit the assets/schema_input.json and the subworkflows/local/utils_nfcore_my_pipeline to match the structure of your samplesheet."

3

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