diff --git a/bin/ms2rescore_cli.py b/bin/ms2rescore_cli.py
index 449c8db3..07ab397e 100755
--- a/bin/ms2rescore_cli.py
+++ b/bin/ms2rescore_cli.py
@@ -135,7 +135,7 @@ def filter_out_artifact_psms(
     "-o", "--output_path", help="Path and stem for output file names (default: derive from identification file)"
 )
 @click.option("-l", "--log_level", help="Logging level (default: `info`)", default="info")
-@click.option("-n", "--processes", help="Number of parallel processes available to MS²Rescore", type=int, default=1)
+@click.option("-n", "--processes", help="Number of parallel processes available to MS²Rescore", type=int, default=16)
 @click.option("-f", "--fasta_file", help="Path to FASTA file")
 @click.option(
     "-fg",
diff --git a/modules/local/ms2rescore.nf b/modules/local/ms2rescore.nf
index ca1c8977..904967eb 100644
--- a/modules/local/ms2rescore.nf
+++ b/modules/local/ms2rescore.nf
@@ -2,10 +2,10 @@ process MS2RESCORE {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::ms2rescore=3.0.0"
+    conda "bioconda::ms2rescore=3.0.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ms2rescore:3.0.0--pyhdfd78af_0':
-        'biocontainers/ms2rescore:3.0.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ms2rescore:3.0.1--pyhdfd78af_2':
+        'biocontainers/ms2rescore:3.0.1--pyhdfd78af_2' }"
 
     // userEmulation settings when docker is specified
     containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''