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Move to a function

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This commit is contained in:
James Fellows Yates 2022-09-27 15:46:17 +02:00
parent 43a8aa4405
commit 87edc4569c
1 changed files with 15 additions and 12 deletions
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27
subworkflows/local/input_check.nf
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@ -21,18 +21,7 @@ workflow INPUT_CHECK {
ch_parsed_samplesheet = EIDO_CONVERT.out.samplesheet_converted ch_parsed_samplesheet = EIDO_CONVERT.out.samplesheet_converted
.splitCsv ( header:true, sep:',' ) .splitCsv ( header:true, sep:',' )
.map{ .map { check_missing_and_singleend_autodetect(it) }
// Checks not supported by EIDO(?)
if ( ( it['fastq_1'] != "" || it['fastq_2'] != "" ) && it['fasta'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: FastQ and FastA files cannot be specified together in the same library. Check input samplesheet! Check sample: ${it['sample']}" }
if ( it['fastq_1'] == "" && it['fastq_2'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: Input samplesheet has a missing fastq_1 when fastq_2 is specified. Check sample: ${it['sample']}" }
single_end = it['fastq_2'] == "" ? true : false
it['single_end'] = single_end
[ it ]
}
.flatten()
.branch { .branch {
fasta: it['fasta'] != '' fasta: it['fasta'] != ''
nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE' nanopore: it['instrument_platform'] == 'OXFORD_NANOPORE'
@ -58,6 +47,19 @@ workflow INPUT_CHECK {
versions = ch_versions // channel: [ versions.yml ] versions = ch_versions // channel: [ versions.yml ]
} }
// Function to validate input sheet and auto-detect R1/R2
def check_missing_and_singleend_autodetect(LinkedHashMap row) {
// Checks not supported by EIDO(?)
if ( ( row['fastq_1'] != "" || row['fastq_2'] != "" ) && row['fasta'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: FastQ and FastA files cannot be specified together in the same library. Check input samplesheet! Check sample: ${row['sample']}" }
if ( row['fastq_1'] == "" && row['fastq_2'] != "" ) { exit 1, "[nf-core/taxprofiler] ERROR: Input samplesheet has a missing fastq_1 when fastq_2 is specified. Check sample: ${row['sample']}" }
single_end = row['fastq_2'] == "" ? true : false
row['single_end'] = single_end
return row
}
// 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
@ -90,6 +92,7 @@ def create_fastq_channel(LinkedHashMap row) {
} }
return fastq_meta return fastq_meta
}// Function to get list of [ meta, fasta ] }// Function to get list of [ meta, fasta ]
def create_fasta_channel(LinkedHashMap row) { def create_fasta_channel(LinkedHashMap row) {
def meta = [:] def meta = [:]