From 9ef97beaef840b84c178ecfdb153b5c44274ad50 Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Tue, 20 Jun 2023 11:11:18 +0200
Subject: [PATCH] =?UTF-8?q?Contr=C3=B4le=20qualit=C3=A9=20et=20basecalling?=
=?UTF-8?q?=20en=20mode=20gpu?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
src/bolero.nf | 8 +++--
src/nextflow.config | 61 +++++++++++++++++---------------
src/nf_modules/ont-guppy/main.nf | 4 ++-
src/nf_modules/pycoqc/main.nf | 21 +++++++++++
4 files changed, 63 insertions(+), 31 deletions(-)
create mode 100644 src/nf_modules/pycoqc/main.nf
diff --git a/src/bolero.nf b/src/bolero.nf
index 0e7e3fa..5c37e4d 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -92,6 +92,7 @@ params.num_callers = 16
params.chunks_per_runner = 512
params.chunk_size = 1900
+
/* Params out */
params.basecalling_out = "01_Basecalling/"
@@ -171,6 +172,7 @@ if(!params.skipBC) {
}
}
+include { pycoqc } from "./nf_modules/pycoqc/main.nf"
include { concatenate } from "./nf_modules/seqkit/main.nf"
include { cut_5pRACE } from "./nf_modules/cutadapt/main.nf"
include { hbv_genome } from "./nf_modules/minimap2/main.nf"
@@ -192,9 +194,9 @@ include { rna_count } from "./nf_modules/rna_count/main.nf"
*/
workflow {
-
//######################## BASECALLING ########################
+
if(params.skipBC) { // we take fastq files as input and skip basecalling
concatenate(barcodes)
}
@@ -204,10 +206,12 @@ workflow {
if(params.gpu_mode) {
basecall_fast5_gpu(input)
concatenate(basecall_fast5_gpu.out.pass)
+ pycoqc(basecall_fast5_gpu.sequencing_summary)
}
else {
basecall_fast5_cpu(input)
concatenate(basecall_fast5_cpu.out.pass)
+ pycoqc(basecall_fast5_cpu.sequencing_summary)
}
}
@@ -241,5 +245,5 @@ workflow {
//#################### VARIANTS D'EPISSAGE ####################
rna_count(junctions_nanosplicer.out.identified_SPvariants, start_position_individuals.out.classification_of_reads)
-
+*/
}
diff --git a/src/nextflow.config b/src/nextflow.config
index e544f2f..b1b3d86 100755
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -72,37 +72,42 @@ profiles {
}
}
}
+
pollux {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- singularity.runOptions = "--bind /data,/home"
- process {
- errorStrategy = 'finish'
- memory = '32GB'
- withLabel: big_mem_mono_cpus {
- cpus = 1
- }
- withLabel: big_mem_multi_cpus {
- cpus = 16
- }
- withLabel: small_mem_mono_cpus {
- cpus = 1
- memory = '2GB'
- }
- withLabel: small_mem_multi_cpus {
- cpus = 8
- memory = '2GB'
- }
- withLabel: mid_mem_mono_cpus {
- cpus = 1
- memory = '8GB'
- }
- withLabel: mid_mem_multi_cpus {
- cpus = 8
- memory = '8GB'
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ singularity.runOptions = "--bind /data,/home"
+ process {
+ errorStrategy = 'finish'
+ memory = '256GB'
+ withLabel: big_mem_mono_cpus {
+ cpus = 1
+ }
+ withLabel: big_mem_multi_cpus {
+ cpus = 16
+ }
+ withLabel: small_mem_mono_cpus {
+ cpus = 1
+ memory = '2GB'
+ }
+ withLabel: small_mem_multi_cpus {
+ cpus = 8
+ memory = '2GB'
+ }
+ withLabel: mid_mem_mono_cpus {
+ cpus = 1
+ memory = '8GB'
+ }
+ withLabel: mid_mem_multi_cpus {
+ cpus = 8
+ memory = '8GB'
+ }
+ withLabel: gpus {
+ maxForks = 1
+ containerOptions = '--nv'
+ }
}
}
- }
singularity {
singularity.enabled = true
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index 7169b7a..d806d33 100644
--- a/src/nf_modules/ont-guppy/main.nf
+++ b/src/nf_modules/ont-guppy/main.nf
@@ -1,6 +1,7 @@
version = "6.4.6"
container_url = "xgrand/ont-guppy:${version}"
+params.config_file = ""
params.basecalling_out = ""
params.flowcell = "FLO-MIN106"
params.kit = "SQK-PBK004"
@@ -51,7 +52,8 @@ guppy_basecaller --compress_fastq \
--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}
+ --chunks_per_runner ${params.chunks_per_runner} \
+ ${params.config_file}
"""
}
diff --git a/src/nf_modules/pycoqc/main.nf b/src/nf_modules/pycoqc/main.nf
new file mode 100644
index 0000000..1951dbf
--- /dev/null
+++ b/src/nf_modules/pycoqc/main.nf
@@ -0,0 +1,21 @@
+version = "2.5.2"
+container_url = "xgrand/pycoqc:${version}"
+
+process pycoqc {
+ container = "${container_url}"
+ label "small_mem_mono_cpus"
+
+ if (params.basecalling_out != "") {
+ publishDir "results/${params.basecalling_out}", mode: 'copy'
+ }
+
+ input:
+ path(txt)
+
+ output:
+ path("*.html")
+
+ """
+ pycoQC -f ${txt} -o quality_control.html)
+ """
+}
\ No newline at end of file
--
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