diff --git a/modules.json b/modules.json
index f3bd866a..e582b8c7 100644
--- a/modules.json
+++ b/modules.json
@@ -17,12 +17,12 @@
                     },
                     "bcftools/filter": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "bd4e0df3319c171072d09dade42e3c06fa373779",
                         "installed_by": ["modules"]
                     },
                     "bcftools/merge": {
                         "branch": "master",
-                        "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
+                        "git_sha": "f7219b428dc69f93aa19f219fb7ce8eae8720400",
                         "installed_by": ["modules"]
                     },
                     "bcftools/norm": {
@@ -82,7 +82,7 @@
                     },
                     "deepvariant": {
                         "branch": "master",
-                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
                         "installed_by": ["modules"]
                     },
                     "eklipse": {
@@ -97,7 +97,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
                         "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
@@ -107,7 +107,7 @@
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filtermutectcalls": {
@@ -137,7 +137,7 @@
                     },
                     "gatk4/printreads": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/revertsam": {
@@ -152,17 +152,17 @@
                     },
                     "gatk4/selectvariants": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/shiftfasta": {
                         "branch": "master",
-                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/splitintervals": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/variantfiltration": {
@@ -212,7 +212,7 @@
                     },
                     "manta/germline": {
                         "branch": "master",
-                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "git_sha": "80dbd95c558a0ebb2123d95f50c093a7f714a0d7",
                         "installed_by": ["modules"]
                     },
                     "mosdepth": {
@@ -297,7 +297,7 @@
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
@@ -332,7 +332,7 @@
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "01b3b2509d76625b6d6cd613b349fb4777712a15",
+                        "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
@@ -352,7 +352,7 @@
                     },
                     "ucsc/wigtobigwig": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
                         "installed_by": ["modules"]
                     },
                     "untar": {
diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf
index 07f33a2e..099eedc7 100644
--- a/modules/nf-core/bcftools/filter/main.nf
+++ b/modules/nf-core/bcftools/filter/main.nf
@@ -11,8 +11,8 @@ process BCFTOOLS_FILTER {
     tuple val(meta), path(vcf)
 
     output:
-    tuple val(meta), path("*.gz"), emit: vcf
-    path  "versions.yml"         , emit: versions
+    tuple val(meta), path("*.${extension}"), emit: vcf
+    path  "versions.yml"                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,9 +20,19 @@ process BCFTOOLS_FILTER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+
+    extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
+
+    if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     """
     bcftools filter \\
-        --output ${prefix}.vcf.gz \\
+        --output ${prefix}.${extension} \\
+        --threads ${task.cpus} \\
         $args \\
         $vcf
 
@@ -35,8 +45,16 @@ process BCFTOOLS_FILTER {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
 
+    extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
+
+    if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     """
-    touch ${prefix}.vcf.gz
+    touch ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf
index 76b35345..eec740ed 100644
--- a/modules/nf-core/bcftools/merge/main.nf
+++ b/modules/nf-core/bcftools/merge/main.nf
@@ -27,16 +27,17 @@ process BCFTOOLS_MERGE {
     def regions = bed ? "--regions-file $bed" : ""
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                     args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                     args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf.gz"
+                    "vcf"
 
     """
     bcftools merge \\
+        $args \\
         $regions \\
         --threads $task.cpus \\
         --output ${prefix}.${extension} \\
-        $args \\
-        *.vcf.gz
+        $vcfs
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -49,8 +50,9 @@ process BCFTOOLS_MERGE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                     args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                     args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-                    "vcf.gz"
+                    "vcf"
     """
     touch ${prefix}.${extension}
 
diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf
index 2cea90ab..1a24ba34 100644
--- a/modules/nf-core/deepvariant/main.nf
+++ b/modules/nf-core/deepvariant/main.nf
@@ -2,7 +2,7 @@ process DEEPVARIANT {
     tag "$meta.id"
     label 'process_high'
 
-    container "docker.io/google/deepvariant:1.5.0"
+    container "nf-core/deepvariant:1.5.0"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 07d5e433..249f9064 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -29,7 +29,11 @@ process FASTQC {
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
-    fastqc $args --threads $task.cpus $renamed_files
+
+    fastqc \\
+        $args \\
+        --threads $task.cpus \\
+        $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
index 41abb235..15a86bea 100644
--- a/modules/nf-core/gatk4/createsequencedictionary/main.nf
+++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf
@@ -20,7 +20,7 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     script:
     def args = task.ext.args ?: ''
 
-    def avail_mem = 6
+    def avail_mem = 6144
     if (!task.memory) {
         log.info '[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
     } else {
diff --git a/modules/nf-core/gatk4/printreads/main.nf b/modules/nf-core/gatk4/printreads/main.nf
index 0fd13048..084d0b46 100644
--- a/modules/nf-core/gatk4/printreads/main.nf
+++ b/modules/nf-core/gatk4/printreads/main.nf
@@ -25,6 +25,7 @@ process GATK4_PRINTREADS {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
+
     def avail_mem = 3072
     if (!task.memory) {
         log.info '[GATK PrintReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -34,7 +35,6 @@ process GATK4_PRINTREADS {
     if ("${input}" == "${prefix}.${input.extension}") {
         error("Output filename is the same as input filename. Please specify a different prefix.")
     }
-
     """
     gatk --java-options "-Xmx${avail_mem}M" PrintReads \\
         $args \\
diff --git a/modules/nf-core/gatk4/selectvariants/main.nf b/modules/nf-core/gatk4/selectvariants/main.nf
index 6c08c3b5..609cb8cc 100644
--- a/modules/nf-core/gatk4/selectvariants/main.nf
+++ b/modules/nf-core/gatk4/selectvariants/main.nf
@@ -22,6 +22,7 @@ process GATK4_SELECTVARIANTS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def interval = intervals ? "--intervals ${intervals}" : ""
+
     def avail_mem = 3072
     if (!task.memory) {
         log.info '[GATK SelectVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf
index cf984e8b..ab0e578c 100644
--- a/modules/nf-core/gatk4/shiftfasta/main.nf
+++ b/modules/nf-core/gatk4/shiftfasta/main.nf
@@ -28,6 +28,7 @@ process GATK4_SHIFTFASTA {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def seq_dict = dict ? "--sequence-dictionary ${dict}" : ""
+
     def avail_mem = 3072
     if (!task.memory) {
         log.info '[GATK ShiftFasta] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
diff --git a/modules/nf-core/gatk4/splitintervals/main.nf b/modules/nf-core/gatk4/splitintervals/main.nf
index df5d0be1..3cb18373 100644
--- a/modules/nf-core/gatk4/splitintervals/main.nf
+++ b/modules/nf-core/gatk4/splitintervals/main.nf
@@ -31,7 +31,6 @@ process GATK4_SPLITINTERVALS {
     } else {
         avail_mem = (task.memory.mega*0.8).intValue()
     }
-
     """
     gatk --java-options "-Xmx${avail_mem}M" SplitIntervals \\
         --output ${prefix} \\
diff --git a/modules/nf-core/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf
index 8f785fe0..e052b7c9 100644
--- a/modules/nf-core/manta/germline/main.nf
+++ b/modules/nf-core/manta/germline/main.nf
@@ -1,6 +1,7 @@
 process MANTA_GERMLINE {
     tag "$meta.id"
     label 'process_medium'
+    label 'error_retry'
 
     conda "bioconda::manta=1.6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
index 1e5181d4..2b7753fd 100644
--- a/modules/nf-core/samtools/sort/main.nf
+++ b/modules/nf-core/samtools/sort/main.nf
@@ -21,13 +21,11 @@ process SAMTOOLS_SORT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def sort_memory = (task.memory.mega/task.cpus).intValue()
     if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools sort \\
         $args \\
         -@ $task.cpus \\
-        -m ${sort_memory}M \\
         -o ${prefix}.bam \\
         -T $prefix \\
         $bam
diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
index fef528fc..d6c5a760 100644
--- a/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -5,7 +5,7 @@ process TABIX_BGZIPTABIX {
     conda "bioconda::tabix=1.11"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
-        'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
+        'biocontainers/tabix:1.11--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/ucsc/wigtobigwig/main.nf b/modules/nf-core/ucsc/wigtobigwig/main.nf
index 493cf578..c5f215b1 100644
--- a/modules/nf-core/ucsc/wigtobigwig/main.nf
+++ b/modules/nf-core/ucsc/wigtobigwig/main.nf
@@ -3,10 +3,10 @@ process UCSC_WIGTOBIGWIG {
     label 'process_single'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda "bioconda::ucsc-wigtobigwig=377"
+    conda "bioconda::ucsc-wigtobigwig=447"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2' :
-        'biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2' }"
+        'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:447--h2a80c09_1' :
+        'biocontainers/ucsc-wigtobigwig:447--h2a80c09_1' }"
 
     input:
     tuple val(meta), path(wig)
@@ -22,7 +22,7 @@ process UCSC_WIGTOBIGWIG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '447' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     wigToBigWig \\
         $args \\
@@ -38,7 +38,7 @@ process UCSC_WIGTOBIGWIG {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '447' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.bw
 
diff --git a/modules/nf-core/ucsc/wigtobigwig/meta.yml b/modules/nf-core/ucsc/wigtobigwig/meta.yml
index a597fde0..470967db 100644
--- a/modules/nf-core/ucsc/wigtobigwig/meta.yml
+++ b/modules/nf-core/ucsc/wigtobigwig/meta.yml
@@ -3,6 +3,7 @@ description: Convert ascii format wig file to binary big wig format
 keywords:
   - wig
   - bigwig
+  - ucsc
 tools:
   - ucsc:
       description: |