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taxprofiler/subworkflows/local/input_check.nf
2022-02-18 07:55:14 +01:00

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//
// Check input samplesheet and get read channels
//
include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
workflow INPUT_CHECK {
take:
samplesheet // file: /path/to/samplesheet.csv
main:
SAMPLESHEET_CHECK ( samplesheet )
.csv
.splitCsv ( header:true, sep:',' )
.map { create_fastq_channels(it) }
.set { reads }
emit:
reads // channel: [ val(meta), [ reads ] ]
versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
}
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
def create_fastq_channels(LinkedHashMap row) {
def meta = [:]
meta.id = row.sample
meta.single_end = row.single_end.toBoolean()
def array = []
if (!file(row.fastq_1).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
}
if (meta.single_end) {
array = [ meta, [ file(row.fastq_1) ] ]
} else {
if (!file(row.fastq_2).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
}
array = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
}
return array
}