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style: use subMap and early returns

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This commit is contained in:
Moritz E. Beber 2023-03-07 13:25:24 +01:00
parent 0bcea6c993
commit d17dce5590
1 changed files with 12 additions and 21 deletions
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29
subworkflows/local/input_check.nf
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@ -37,49 +37,40 @@ workflow INPUT_CHECK {
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
def create_fastq_channel(LinkedHashMap row) { def create_fastq_channel(LinkedHashMap row) {
// create meta map // create meta map
def meta = [:] def meta = row.subMap(['sample', 'run_accession', 'instrument_platform'])
meta.id = row.sample
meta.run_accession = row.run_accession
meta.instrument_platform = row.instrument_platform
meta.single_end = row.single_end.toBoolean() meta.single_end = row.single_end.toBoolean()
meta.is_fasta = false meta.is_fasta = false
// add path(s) of the fastq file(s) to the meta map // add path(s) of the fastq file(s) to the meta map
def fastq_meta = []
if (!file(row.fastq_1).exists()) { if (!file(row.fastq_1).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}"
} }
if (meta.single_end) { if (meta.single_end) {
fastq_meta = [ meta, [ file(row.fastq_1) ] ] return [ meta, [ file(row.fastq_1) ] ]
} else { } else {
if (meta.instrument_platform == 'OXFORD_NANOPORE') { if (meta.instrument_platform == 'OXFORD_NANOPORE') {
if (row.fastq_2 != '') { if (row.fastq_2 != '') {
exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}" exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}"
} }
fastq_meta = [ meta, [ file(row.fastq_1) ] ] return [ meta, [ file(row.fastq_1) ] ]
} else { } else {
if (!file(row.fastq_2).exists()) { if (!file(row.fastq_2).exists()) {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}"
} }
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] return [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
} }
}
}
} // Function to get list of [ meta, fasta ]
return fastq_meta
}// Function to get list of [ meta, fasta ]
def create_fasta_channel(LinkedHashMap row) { def create_fasta_channel(LinkedHashMap row) {
def meta = [:] def meta = row.subMap(['sample', 'run_accession', 'instrument_platform'])
meta.id = row.sample
meta.run_accession = row.run_accession
meta.instrument_platform = row.instrument_platform
meta.single_end = true meta.single_end = true
meta.is_fasta = true meta.is_fasta = true
def array = []
if (!file(row.fasta).exists()) { if (!file(row.fasta).exists()) {
exit 1, "ERROR: Please check input samplesheet -> FastA file does not exist!\n${row.fasta}" exit 1, "ERROR: Please check input samplesheet -> FastA file does not exist!\n${row.fasta}"
} }
array = [ meta, [ file(row.fasta) ] ] return [ meta, [ file(row.fasta) ] ]
return array
} }