From 3856bdcfd2a0ec20f90179c19f216f16f3d3320e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 29 Mar 2023 14:22:36 +0200
Subject: [PATCH] update config
---
src/modules/fastkmers.nf | 1 +
src/nextflow.config | 80 ++++++++++++++++++++++------------------
2 files changed, 46 insertions(+), 35 deletions(-)
diff --git a/src/modules/fastkmers.nf b/src/modules/fastkmers.nf
index 5a77b0a..4384f0b 100644
--- a/src/modules/fastkmers.nf
+++ b/src/modules/fastkmers.nf
@@ -4,6 +4,7 @@
process FASTKMERS {
tag "$meta.id"
label 'process_single'
+ publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
container "lbmc/fastkmers:025efdf"
diff --git a/src/nextflow.config b/src/nextflow.config
index 915cac7..54b4f32 100644
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -1,39 +1,49 @@
-psmn {
- charliecloud.enabled = true
- charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
- charliecloud.readOnlyInputs = true
- charliecloud.runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
+nextflowVersion = '>=20'
- process{
- errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
- maxRetries = 3
- executor = "slurm"
- queue = "Lake"
- withLabel: process_single {
- cpus = 1
- memory = "128GB"
- time = "24h"
- }
- withLabel: big_mem_multi_cpus {
- cpus = 32
- memory = "192GB"
- time = "24h"
- }
- withLabel: small_mem_mono_cpus {
- cpus = 1
- memory = "16GB"
- time = "24h"
- }
- withLabel: small_mem_multi_cpus {
- cpus = 32
- memory = "16GB"
- time = "24h"
- }
- }
+manifest {
+ homePage = 'https://gitbio.ens-lyon.fr/LBMC/Delattre/kmer-diff'
+ description = 'pipeline to quantify kmers'
+ mainScript = 'main.nf'
+ version = '0.0.1'
+}
+
+report {
+ enabled = true
+ file = "$baseDir/../results/report.html"
+}
- params {
- max_memory = 512.GB
- max_cpus = 32
- max_time = 24.h
+profiles {
+ psmn {
+ charliecloud.enabled = true
+ charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
+ charliecloud.readOnlyInputs = true
+ charliecloud.runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs --bind /home:/home"
+
+ process{
+ errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
+ maxRetries = 3
+ executor = "slurm"
+ queue = "Lake"
+ withLabel: process_single {
+ cpus = 1
+ memory = "128GB"
+ time = "24h"
+ }
+ withLabel: big_mem_multi_cpus {
+ cpus = 32
+ memory = "192GB"
+ time = "24h"
+ }
+ withLabel: small_mem_mono_cpus {
+ cpus = 1
+ memory = "16GB"
+ time = "24h"
+ }
+ withLabel: small_mem_multi_cpus {
+ cpus = 32
+ memory = "16GB"
+ time = "24h"
+ }
+ }
}
}
--
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