Fixed sample sheet check error (278d59f1) · Commits · Chaos / Cutandrun

subworkflows/local/input_check.nf

+25 −2

Original line number	Diff line number	Diff line
		@@ -4,7 +4,6 @@

		params.options = [:]

		include {get_samplesheet_paths } from "./test"
		include { SAMPLESHEET_CHECK } from "../../modules/local/python/samplesheet_check" addParams( options: params.options )

		workflow INPUT_CHECK {
		@@ -20,3 +19,27 @@ workflow INPUT_CHECK {
		emit:
		reads // channel: [ val(meta), [ reads ] ]
		}

		// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
		def get_samplesheet_paths(LinkedHashMap row) {
		def meta = [:]
		meta.id = row.id
		meta.group = row.group
		meta.replicate = row.replicate.toInteger()
		meta.control_group = row.control_group.toInteger()
		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
		}

deleted100644 → 0

+0 −23

Original line number	Diff line number	Diff line
		// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
		def get_samplesheet_paths(LinkedHashMap row) {
		def meta = [:]
		meta.id = row.id
		meta.group = row.group
		meta.replicate = row.replicate.toInteger()
		meta.control_group = row.control_group.toInteger()
		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
		}
		No newline at end of file