From 0ee2e222dc72876a953badf1152d537b4b57aef5 Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Thu, 22 Jun 2023 10:03:53 +0200
Subject: [PATCH] Correction des erreurs du process barcoding
---
src/nf_modules/ont-guppy/main.nf | 43 ++++++++++++++++++++++++++------
1 file changed, 36 insertions(+), 7 deletions(-)
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index c4f8278..f9f6aed 100644
--- a/src/nf_modules/ont-guppy/main.nf
+++ b/src/nf_modules/ont-guppy/main.nf
@@ -12,7 +12,7 @@ params.chunks_per_runner = 1
options = ""
process basecall_fast5_gpu {
container = "${container_url}"
- label "gpu"
+ label "gpus"
tag "$fast5_folder"
if (params.basecalling_out != "") {
publishDir "results/${params.basecalling_out}", mode: 'copy'
@@ -64,6 +64,7 @@ guppy_basecaller --compress_fastq \
"""
}
+// A modifier quand le process gpu marchera
process basecall_fast5_cpu {
container = "${container_url}"
label "big_mem_multi_cpus"
@@ -106,7 +107,36 @@ guppy_basecaller --compress_fastq \
"""
}
-process barcoding {
+params.kit_barcoding = "EXP-PBC001"
+process barcoding_gpu {
+ container = "${container_url}"
+ label "gpus"
+ tag "$fast5_folder"
+ if (params.barcoding_out != "") {
+ publishDir "results/${params.barcoding_out}", mode: 'copy'
+ }
+
+ input:
+ path(pass_path)
+
+ output:
+ path("*")
+
+ script:
+"""
+guppy_barcoder \
+ --input_path ${pass_path} \
+ --save_path . \
+ -t ${params.gpu_threads_per_caller} \
+ --barcode_kits ${params.kit_barcoding} \
+ --progress_stats_frequency 60 \
+ --enable_trim_barcodes \
+ --trim_adapters \
+ --compress_fastq
+"""
+}
+
+process barcoding_cpu {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$fast5_folder"
@@ -118,17 +148,16 @@ process barcoding {
path(pass_path)
output:
- path("barcode")
+ path("*")
script:
"""
guppy_barcoder \
--input_path ${pass_path} \
- --save_path barcode/ \
- -c /opt/ont/guppy/data/${params.config_file} \
- --barcode_kits ${params.kit} \
+ --save_path . \
+ -t ${task.cpus} \
+ --barcode_kits ${params.kit_barcoding} \
--progress_stats_frequency 60 \
- -x "cuda:all" \
--enable_trim_barcodes \
--trim_adapters \
--compress_fastq
--
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