From 9f526a98fe4e692b02f75d087d2b39bd6fccccfe Mon Sep 17 00:00:00 2001
From: aliarifki <aliarifki@outlook.fr>
Date: Fri, 16 Jun 2023 15:08:54 +0200
Subject: [PATCH] modification du profile pollux
---
src/nextflow.config | 2 +-
src/nf_modules/ont-guppy/main.nf | 9 +++++----
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/src/nextflow.config b/src/nextflow.config
index 54e515f..9a1b44e 100755
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -75,7 +75,7 @@ profiles {
pollux {
singularity.enabled = true
singularity.cacheDir = "./bin/"
- singularity.bind = "/home"
+ singularity.runOptions = "--bind /data,/home"
process {
errorStrategy = 'finish'
memory = '32GB'
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index 19aecb1..ff9ba5c 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 {
}
input:
- val(fast5_folder)
+ path(fast5_folder)
output:
path "pass", emit: pass
@@ -39,10 +39,11 @@ process basecall_fast5_gpu {
"""
echo "Start basecalling using GPUs."
# guppy_basecaller --print_workflows
-find -type f -name "*.fast5" > allfast5files.txt
+path=\$(readlink -f ${fast5_folder})
+find \${path} -type f -name "*.fast5" > allfast5files.txt
guppy_basecaller --compress_fastq \
- -i ${fast5_folder} \
- --input_file_list allfast5files.txt \
+ -i / \
+ --input_file_list fichier.txt \
-s . \
--flowcell ${params.flowcell} \
--kit ${params.kit} \
--
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