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