millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-21 20:26:03 +00:00
Code Issues Releases Packages Activity

style: use subMap and early returns

Browse source
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
Show stats Download patch file Download diff file Expand all files Collapse all files

33
subworkflows/local/input_check.nf
View file

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