poreCov
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update guppy
new guppy version 6 does not require arrangement files for demultiplexing and has some changes
demulti like this
process collect_fastq {
label 'demultiplex'
input:
tuple val(name), val(technology), path(dir)
output:
tuple val(name), path("*.fastq.gz"), emit: reads
script:
if (params.single)
"""
find -L ${dir} -name '*.fastq' -exec cat {} + | gzip > ${name}.fastq.gz
find -L ${dir} -name '*.fastq.gz' -exec zcat {} + | gzip >> ${name}.fastq.gz
"""
else if (!params.single)
"""
BARCODE_DIRS=\$(find -L ${dir} -name "barcode??" -type d)
if [ -z "\${BARCODE_DIRS}" ]; then
guppy_barcoder -t ${task.cpus} -r -i ${dir} -s fastq_outbreak \
--detect_mid_strand_barcodes \
--min_score_barcode_mid 50 \
--trim_adapters \
--trim_barcodes \
--disable_pings
for barcodes in fastq_outbreak/barcode??; do
find -L \${barcodes} -name '*.fastq' -exec cat {} + | gzip >> \${barcodes##*/}.fastq.gz
done
else
for barcodes in \${BARCODE_DIRS}; do
find -L \${barcodes} -name '*.fastq' -exec cat {} + | gzip >> \${barcodes##*/}.fastq.gz
find -L \${barcodes} -name '*.fastq.gz' -exec zcat {} + | gzip >> \${barcodes##*/}.fastq.gz
done
fi
"""
stub:
"""
touch ${name}.fastq.gz
"""
}