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style: use subMap and early returns
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1 changed files with 12 additions and 21 deletions
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@ -37,49 +37,40 @@ workflow INPUT_CHECK {
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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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def meta = row.subMap(['sample', 'run_accession', '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${row.fastq_1}"
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}
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if (meta.single_end) {
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fastq_meta = [ meta, [ file(row.fastq_1) ] ]
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return [ meta, [ file(row.fastq_1) ] ]
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} else {
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if (meta.instrument_platform == 'OXFORD_NANOPORE') {
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if (row.fastq_2 != '') {
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exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}"
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}
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fastq_meta = [ meta, [ file(row.fastq_1) ] ]
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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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exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
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}
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fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
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return [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
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}
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}
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}
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}
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return fastq_meta
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}// Function to get list of [ meta, fasta ]
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// Function to get list of [ meta, fasta ]
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def create_fasta_channel(LinkedHashMap row) {
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def meta = [:]
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meta.id = row.sample
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meta.run_accession = row.run_accession
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meta.instrument_platform = row.instrument_platform
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def meta = row.subMap(['sample', 'run_accession', 'instrument_platform'])
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meta.single_end = true
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meta.is_fasta = true
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def array = []
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if (!file(row.fasta).exists()) {
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exit 1, "ERROR: Please check input samplesheet -> FastA file does not exist!\n${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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return [ meta, [ file(row.fasta) ] ]
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}
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