From f7ba52a88600dc2d5ef0639b36cda5dcb281aeba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Noirot=20C=C3=A9line?= <celine.noirot@inra.fr>
Date: Mon, 10 Feb 2025 16:46:09 +0100
Subject: [PATCH] Upgrade cutadapt to 5.0
---
conf/base.config | 1 +
conf/test.config | 1 -
env/metagWGS.yml | 1 -
3 files changed, 1 insertion(+), 2 deletions(-)
diff --git a/conf/base.config b/conf/base.config
index 768c2dc..d76da67 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -17,6 +17,7 @@ process {
maxErrors = '-1'
withName: CUTADAPT {
+ container = 'quay.io/biocontainers/cutadapt:5.0--py310h1fe012e_0'
cpus = 8
memory = { 8.GB * task.attempt }
}
diff --git a/conf/test.config b/conf/test.config
index cd3005c..9bac780 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -18,7 +18,6 @@ process {
memory = { 2.GB * task.attempt }
}
withName: MULTIQC {
- container = 'quay.io/biocontainers/multiqc:1.27.1--pyhdfd78af_0'
executor = "local"
memory = { 2.GB * task.attempt }
}
diff --git a/env/metagWGS.yml b/env/metagWGS.yml
index dbde1c5..cb02fd8 100644
--- a/env/metagWGS.yml
+++ b/env/metagWGS.yml
@@ -8,7 +8,6 @@ dependencies:
- bcbio-gff=0.6.9
- bwa-mem2=2.2.1
- cd-hit=4.8.1
- - cutadapt=4.2
- diamond=2.0.15
- eggnog-mapper=2.1.9
- fastqc=0.11.9
--
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