From 8fc859a028453696991623c4b717d17d0b61b291 Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Thu, 22 Jun 2023 11:24:08 +0200
Subject: [PATCH] Correction de la fonction basecalling gpu
---
src/bolero.nf | 16 ++++++++++------
src/nf_modules/ont-guppy/main.nf | 9 +++++----
2 files changed, 15 insertions(+), 10 deletions(-)
diff --git a/src/bolero.nf b/src/bolero.nf
index 52f67da..f0861d0 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -157,12 +157,12 @@ Channel
.map(it -> [it.baseName, it])
.set{barcodes}
-
+/*
// Test pour barcoding process
Channel
.fromPath(params.pass)
.set{pass}
-
+*/
/*
****************************************************************
Imports
@@ -204,11 +204,13 @@ include { rna_count } from "./nf_modules/rna_count/main.nf"
*/
workflow {
+ /*
pass.view()
barcoding_cpu(pass)
+ */
//######################## BASECALLING ########################
-/*
+
if(params.skipBC) { // we take fastq files as input and skip basecalling
concatenate(barcodes)
}
@@ -217,18 +219,20 @@ workflow {
else { // we take fast5 files as input and proceed to basecalling with guppy
if(params.gpu_mode) {
basecall_fast5_gpu(input)
- concatenate(basecall_fast5_gpu.out.pass)
+ barcoding_gpu(basecall_fast5_gpu.out.pass)
+ //concatenate(basecall_fast5_gpu.out.pass)
control_basecalling(basecall_fast5_gpu.sequencing_summary)
}
else {
basecall_fast5_cpu(input)
- concatenate(basecall_fast5_cpu.out.pass)
+ barcoding_cpu(basecall_fast5_cpu.out.pass)
+ //concatenate(basecall_fast5_cpu.out.pass)
control_basecalling(basecall_fast5_cpu.sequencing_summary)
}
}
-
+/*
//####################### PREPROCESSING #######################
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index f9f6aed..a4f118e 100644
--- a/src/nf_modules/ont-guppy/main.nf
+++ b/src/nf_modules/ont-guppy/main.nf
@@ -27,7 +27,7 @@ process basecall_fast5_gpu {
errorKit "WARNING ! No kit type given..."
errorKit.view()
}
-
+/*
if (params.config_file != "") {
options = "-c /opt/ont/guppy/data/${params.config_file}"
}
@@ -35,7 +35,7 @@ process basecall_fast5_gpu {
options = "--flowcell ${params.flowcell} \
--kit ${params.kit} "
}
-
+*/
input:
path(fast5_folder)
@@ -53,14 +53,15 @@ path=\$(readlink -f ${fast5_folder})
find \${path} -type f -name "*.fast5" > allfast5files.txt
guppy_basecaller --compress_fastq \
-i / \
- --input_file_list fichier.txt \
+ --input_file_list allfast5files.txt \
-s . \
-x "cuda:all" \
--min_qscore ${params.min_qscore} \
--gpu_runners_per_device ${params.gpu_runners_per_device} \
--num_callers ${params.num_callers} \
--chunks_per_runner ${params.chunks_per_runner} \
- ${options}
+ --flowcell ${params.flowcell} \
+ --kit ${params.kit}
"""
}
--
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