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93 lines
3.4 KiB
Text
93 lines
3.4 KiB
Text
//
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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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include { EIDO_VALIDATE } from '../../modules/nf-core/modules/eido/validate/main'
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include { EIDO_CONVERT } from '../../modules/nf-core/modules/eido/convert/main'
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workflow INPUT_CHECK {
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take:
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samplesheet_or_pep_config // file: /path/to/samplesheet.csv or /path/to/pep/config.yaml
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pep_input_base_dir
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main:
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EIDO_VALIDATE ( samplesheet_or_pep_config, file("$projectDir/assets/samplesheet_schema.yaml"), pep_input_base_dir )
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converted_samplesheet = EIDO_CONVERT ( samplesheet_or_pep_config, "csv", pep_input_base_dir )
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parsed_samplesheet = SAMPLESHEET_CHECK ( converted_samplesheet.samplesheet_converted )
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.csv
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.splitCsv ( header:true, sep:',' )
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.branch {
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fasta: it['fasta'] != ''
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nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
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fastq: true
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}
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parsed_samplesheet.fastq
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.map { create_fastq_channel(it) }
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.set { fastq }
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parsed_samplesheet.nanopore
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.map { create_fastq_channel(it) }
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.set { nanopore }
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parsed_samplesheet.fasta
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.map { create_fasta_channel(it) }
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.set { fasta }
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emit:
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fastq = fastq ?: [] // channel: [ val(meta), [ reads ] ]
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nanopore = nanopore ?: [] // channel: [ val(meta), [ reads ] ]
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fasta = fasta ?: [] // channel: [ val(meta), fasta ]
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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_channel(LinkedHashMap row) {
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// create meta map
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def meta = [:]
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meta.id = row.sample
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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meta.single_end = row.single_end.toBoolean()
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meta.is_fasta = false
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// add path(s) of the fastq file(s) to the meta map
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def fastq_meta = []
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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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fastq_meta = [ meta, [ file(row.fastq_1) ] ]
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} else {
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if (meta.instrument_platform == 'OXFORD_NANOPORE') {
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if (row.fastq_2 != '') {
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exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}"
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}
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fastq_meta = [ meta, [ file(row.fastq_1) ] ]
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} else {
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if (!file(row.fastq_2).exists()) {
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exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
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}
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fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
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}
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}
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return fastq_meta
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}// Function to get list of [ meta, fasta ]
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def create_fasta_channel(LinkedHashMap row) {
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def meta = [:]
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meta.id = row.sample
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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meta.single_end = true
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meta.is_fasta = true
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def array = []
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if (!file(row.fasta).exists()) {
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exit 1, "ERROR: Please check input samplesheet -> FastA file does not exist!\n${row.fasta}"
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}
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array = [ meta, [ file(row.fasta) ] ]
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return array
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}
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