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103 lines
3.5 KiB
Text
103 lines
3.5 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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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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// Table to list, group per sample, detect if sample has multi-run,
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// then spread back to per-run rows but with multi-run info added to meta
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ch_split_samplesheet = SAMPLESHEET_CHECK ( samplesheet )
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.csv
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.splitCsv ( header:true, sep:',' )
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.map{
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row ->
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[ [ row.sample.toString() ], row ]
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}
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.groupTuple()
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.map {
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sample, rows ->
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def is_multirun = rows.size() > 1
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[ rows, is_multirun ]
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}
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.transpose(by: 0)
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.map {
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row, is_multirun ->
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row['is_multirun'] = is_multirun
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return row
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}
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// Split for context-dependent channel generation
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ch_parsed_samplesheet = ch_split_samplesheet
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.branch { row ->
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fasta: row.fasta != ''
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nanopore: row.instrument_platform == 'OXFORD_NANOPORE'
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fastq: true
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}
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// Channel generation
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ch_fastq = ch_parsed_samplesheet.fastq
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.map { create_fastq_channel(it) }
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ch_nanopore = ch_parsed_samplesheet.nanopore
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.map { create_fastq_channel(it) }
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ch_fasta = ch_parsed_samplesheet.fasta
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.map { create_fasta_channel(it) }
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emit:
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fastq = ch_fastq ?: [] // channel: [ val(meta), [ reads ] ]
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nanopore = ch_nanopore ?: [] // channel: [ val(meta), [ reads ] ]
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fasta = ch_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 = row.subMap(['sample', 'run_accession', 'instrument_platform', 'is_multirun'])
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meta.id = meta.sample
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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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if (!file(row.fastq_1).exists()) {
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error("ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}")
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}
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if (meta.single_end) {
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return [ meta, [ file(row.fastq_1) ] ]
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} else {
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if (meta.instrument_platform == 'OXFORD_NANOPORE') {
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if (row.fastq_2 != '') {
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error("ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}")
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}
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return [ meta, [ file(row.fastq_1) ] ]
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} else {
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if (!file(row.fastq_2).exists()) {
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error("ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}")
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}
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return [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
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}
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}
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}
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// Function to get list of [ meta, fasta ]
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def create_fasta_channel(LinkedHashMap row) {
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// don't include multi-run information as we don't do FASTA run merging
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def meta = row.subMap(['sample', 'run_accession', 'instrument_platform' ])
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meta.id = meta.sample
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meta.single_end = true
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meta.is_fasta = true
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if (!file(row.fasta).exists()) {
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error("ERROR: Please check input samplesheet -> FastA file does not exist!\n${row.fasta}")
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}
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return [ meta, [ file(row.fasta) ] ]
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}
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