Newer
Older
// SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
//
// SPDX-License-Identifier: AGPL-3.0-or-later
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
version = "5.0.11"
container_url = "lbmc/guppy-cpu:${version}"
params.basecalling_out = ""
params.flowcell = "FLO-MIN106"
params.kit = "SQK-PCS109"
params.cpu_threads_per_caller = 4
params.num_callers = 1
process basecall_fast5 {
container = "${container_url}"
label "big_mem_multi_cpus"
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 \
-i ${path(fast5)} \
-s ${params.basecalling_out} \
--cpu_threads_per_caller ${params.cpu_threads_per_caller} \
--num_callers ${params.num_callers} \
--flowcell ${params.flowcell} \
--kit ${params.kit}
"""
}