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Add nanopore channel

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This commit is contained in:
ljmesi 2022-03-18 10:47:41 +01:00
parent 0f0ed6cd46
commit 41b3d8db82
1 changed files with 17 additions and 4 deletions
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21
subworkflows/local/input_check.nf
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@ -20,10 +20,15 @@ workflow INPUT_CHECK {
} }
parsed_samplesheet.fastq parsed_samplesheet.fastq
.map { create_fastq_channels(it) } .map { create_fastq_channel(it) }
.dump(tag: "fastq_channel_init") .dump(tag: "fastq_channel_init")
.set { fastq } .set { fastq }
parsed_samplesheet.nanopore
.map { create_fastq_channel(it) }
.dump(tag: "fastq_nanopore_channel_init")
.set { nanopore }
parsed_samplesheet.fasta parsed_samplesheet.fasta
.map { create_fasta_channels(it) } .map { create_fasta_channels(it) }
.dump(tag: "fasta_channel_init") .dump(tag: "fasta_channel_init")
@ -31,6 +36,7 @@ workflow INPUT_CHECK {
emit: emit:
fastq // channel: [ val(meta), [ reads ] ] fastq // channel: [ val(meta), [ reads ] ]
nanopore // channel: [ val(meta), [ reads ] ]
fasta // channel: [ val(meta), fasta ] fasta // channel: [ val(meta), fasta ]
versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
} }
@ -52,10 +58,17 @@ def create_fastq_channel(LinkedHashMap row) {
if (meta.single_end) { if (meta.single_end) {
fastq_meta = [ meta, [ file(row.fastq_1) ] ] fastq_meta = [ meta, [ file(row.fastq_1) ] ]
} else { } else {
if (!file(row.fastq_2).exists()) { if (meta.instrument_platform == 'OXFORD_NANOPORE') {
exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" if (row.fastq_2 != '') {
exit 1, "ERROR: Please check input samplesheet -> For Oxford Nanopore reads Read 2 FastQ should be empty!\n${row.fastq_2}"
}
fastq_meta = [ 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) ] ]
} }
fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ]
} }
return fastq_meta return fastq_meta
} }