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?