diff --git a/conf/modules.config b/conf/modules.config
index bb3ede0a..febd9b16 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -86,4 +86,8 @@ process {
     withName: FILTER_ASSEMBLY {
         ext.args = '--cov_cutoff 1 --len_cutoff 100'
     }
+
+    withName: BAKTA_BAKTA {
+        ext.args = '--force'
+    }
 }
diff --git a/modules/local/bgzip_make_gzip.nf b/modules/local/bgzip_make_gzip.nf
index bd32dc5c..dca34d80 100644
--- a/modules/local/bgzip_make_gzip.nf
+++ b/modules/local/bgzip_make_gzip.nf
@@ -5,7 +5,7 @@ process BGZIP_MAKE_GZIP {
     conda "bioconda::tabix=1.11"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
-        'biocontainers/tabix:1.11--hdfd78af_0' }"
+        'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/bakta/bakta/main.nf b/modules/nf-core/bakta/bakta/main.nf
index 6399f5d0..53dc8d3e 100644
--- a/modules/nf-core/bakta/bakta/main.nf
+++ b/modules/nf-core/bakta/bakta/main.nf
@@ -5,7 +5,7 @@ process BAKTA_BAKTA {
     conda "bioconda::bakta=1.7.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bakta:1.7.0--pyhdfd78af_1' :
-        'biocontainers/bakta:1.7.0--pyhdfd78af_1' }"
+        'quay.io/biocontainers/bakta:1.8.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
index 831b7f12..25c1427c 100644
--- a/modules/nf-core/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -5,7 +5,7 @@ process FASTP {
     conda "bioconda::fastp=0.23.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' :
-        'biocontainers/fastp:0.23.4--h5f740d0_0' }"
+        'biocontainers/fastp:v0.20.1_cv1' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/pirate/main.nf b/modules/nf-core/pirate/main.nf
index f4bb4eb0..370f879d 100644
--- a/modules/nf-core/pirate/main.nf
+++ b/modules/nf-core/pirate/main.nf
@@ -5,7 +5,7 @@ process PIRATE {
     conda "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' :
-        'biocontainers/pirate:1.0.4--hdfd78af_2' }"
+        'quay.io/biocontainers/pirate:1.0.5--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff)
@@ -22,6 +22,10 @@ process PIRATE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    # Rename .gff3 to .gff if needed
+    find -regex .*\\.gff3\$ | sed 's/3\$//' | xargs -I {} mv {}3 {}
+
+    # Run pirate on all .gff in input directory
     PIRATE \\
         $args \\
         --threads $task.cpus \\
diff --git a/modules/nf-core/quast/main.nf b/modules/nf-core/quast/main.nf
index ecfbf406..b8f22d7e 100644
--- a/modules/nf-core/quast/main.nf
+++ b/modules/nf-core/quast/main.nf
@@ -4,7 +4,7 @@ process QUAST {
     conda "bioconda::quast=5.2.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/quast:5.2.0--py39pl5321h2add14b_1' :
-        'biocontainers/quast:5.2.0--py39pl5321h2add14b_1' }"
+        'quay.io/biocontainers/quast:5.2.0--py38pl5321h5cf8b27_3' }"
 
     input:
     path consensus
diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf
index e424a182..f40b4eda 100644
--- a/modules/nf-core/spades/main.nf
+++ b/modules/nf-core/spades/main.nf
@@ -5,7 +5,7 @@ process SPADES {
     conda "bioconda::spades=3.15.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1' :
-        'biocontainers/spades:3.15.5--h95f258a_1' }"
+        'biocontainers/spades:v3.13.1_cv1' }"
 
     input:
     tuple val(meta), path(illumina), path(pacbio), path(nanopore)