From 4ff2145e44d0c5b98f0d90cc43813cb343b2ee55 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 20 Jun 2022 08:23:14 +0200
Subject: [PATCH] Roll back MALT  version

---
 modules.json                             | 2 +-
 modules/nf-core/modules/malt/run/main.nf | 7 +++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/modules.json b/modules.json
index a8f5a57..9561b0f 100644
--- a/modules.json
+++ b/modules.json
@@ -49,7 +49,7 @@
                 "git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
             },
             "malt/run": {
-                "git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
+                "git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"
             },
             "megan/rma2info": {
                 "git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
diff --git a/modules/nf-core/modules/malt/run/main.nf b/modules/nf-core/modules/malt/run/main.nf
index 4e2e50c..2b91d90 100644
--- a/modules/nf-core/modules/malt/run/main.nf
+++ b/modules/nf-core/modules/malt/run/main.nf
@@ -2,10 +2,10 @@ process MALT_RUN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::malt=0.53" : null)
+    conda (params.enable_conda ? "bioconda::malt=0.41" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0' :
-        'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
+        'quay.io/biocontainers/malt:0.41--1' }"
 
     input:
     tuple val(meta), path(fastqs)
@@ -33,7 +33,6 @@ process MALT_RUN {
 
     """
     malt-run \\
-        -J-Xmx${avail_mem}g \\
         -t $task.cpus \\
         -v \\
         -o . \\