You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
45 lines
1.3 KiB
Plaintext
45 lines
1.3 KiB
Plaintext
//
|
|
// 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_channel(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_channel(LinkedHashMap row) {
|
|
// create meta map
|
|
def meta = [:]
|
|
meta.id = row.sample
|
|
meta.single_end = row.single_end.toBoolean()
|
|
|
|
// add path(s) of the fastq file(s) to the meta map
|
|
def fastq_meta = []
|
|
if (!file(row.fastq_1).exists()) {
|
|
exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
|
|
}
|
|
if (meta.single_end) {
|
|
fastq_meta = [ meta, [ file(row.fastq_1) ] ]
|
|
} else {
|
|
if (!file(row.fastq_2).exists()) {
|
|
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
|
|
}
|
|
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
|
|
}
|
|
return fastq_meta
|
|
}
|