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// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
//
// SPDX-License-Identifier: AGPL-3.0-or-later
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version = "5.0.11"
container_url = "lbmc/guppy-gpu:${version}"
params.basecalling_out = ""
params.flowcell = ""
params.kit = ""
params.gpu_runners_per_device = 16
process basecall_fast5 {
container = "${container_url}"
// Need to create a profile using GPUs
label ""
tag "$file_id"
if (params.basecalling_out != "") {
publishDir "results/${params.basecalling_out}", mode: 'copy'
}
if (params.flowcell == "") {
errorFlowcell << "WARNING ! No Flowcell type given..."
errorFlowcell.view()
}
if (params.kit == "") {
errorKit "WARNING ! No kit type given..."
errorKit.view()
}
input:
tuple val(file_id), path(fast5)
output:
tuple val(file_id), path("*.fastq*"), emit: fastq
script:
"""
guppy_basecaller --compress_fastq -x "cuda:all" --min_qscore 7.0 \
-i ${path(fast5)} \
-s ${params.basecalling_out} \
--gpu_runners_per_device ${params.gpu_runners_per_device} \
--flowcell ${params.flowcell} \
--kit ${params.kit}
"""
}