From a59be7fa53134aad54e1d59fb6b772ad33a122f0 Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Tue, 1 Aug 2023 15:19:44 +0200
Subject: [PATCH] Resolution petits bugs
---
src/bolero.nf | 3 +--
src/nextflow.config | 2 +-
src/nf_modules/ont-guppy/main.nf | 14 +++++++-------
3 files changed, 9 insertions(+), 10 deletions(-)
diff --git a/src/bolero.nf b/src/bolero.nf
index 10b213e..edae56a 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -171,7 +171,6 @@ if(!params.skipBC) {
}
// include { barecode } from "./nf_modules/barecode/main.nf"
-include { pycoqc } from "./nf_modules/pycoqc/main.nf"
include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
include { control_bam } from "./nf_modules/pycoqc/main.nf"
@@ -257,7 +256,7 @@ workflow {
sort_index_bam(hbv_genome.out.bam)
//Quality control
- if(params.skipBC == False) {
+ if(params.skipBC == false) {
if(params.gpu_mode) {
control_bam(basecall_fast5_gpu.out.sequencing_summary.collect(), sort_index_bam.out.indexed_bam)
}
diff --git a/src/nextflow.config b/src/nextflow.config
index 870600d..4b6a530 100755
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -112,7 +112,7 @@ profiles {
singularity {
singularity.enabled = true
singularity.cacheDir = "./bin/"
- singularity.bind = "/home"
+ singularity.runOptions = "-B /home"
process {
errorStrategy = 'finish'
memory = '12GB'
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index d4002f1..6c0bdb9 100644
--- a/src/nf_modules/ont-guppy/main.nf
+++ b/src/nf_modules/ont-guppy/main.nf
@@ -129,7 +129,7 @@ process barcoding_gpu {
}
if (params.config_file != "") {
- options = "-c /opt/ont/guppy/data/${params.config_file} \ "
+ options = "-c /opt/ont/guppy/data/${params.config_file}"
}
else {
options = ""
@@ -148,11 +148,11 @@ guppy_barcoder \
--save_path . \
-t ${params.gpu_threads_per_caller} \
--barcode_kits ${params.kit_barcoding} \
- ${options}
--progress_stats_frequency 60 \
--enable_trim_barcodes \
--trim_adapters \
- --compress_fastq
+ --compress_fastq \
+ ${options}
"""
}
@@ -165,7 +165,7 @@ process barcoding_cpu {
}
if (params.config_file != "") {
- options = "-c /opt/ont/guppy/data/${params.config_file} \ "
+ options = "-c /opt/ont/guppy/data/${params.config_file}"
}
else {
options = ""
@@ -185,10 +185,10 @@ guppy_barcoder \
--save_path . \
-t ${task.cpus} \
--barcode_kits ${params.kit_barcoding} \
- ${options}
--progress_stats_frequency 60 \
--enable_trim_barcodes \
--trim_adapters \
- --compress_fastq
+ --compress_fastq \
+ ${options}
"""
-}
\ No newline at end of file
+}
--
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