diff --git a/CHANGELOG.md b/CHANGELOG.md
index fb1b809..ae71456 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,12 +15,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#35](https://github.com/qbic-pipelines/vcftomaf/pull/35) - Template update to 3.2.0 (@famosab)
 - [#37](https://github.com/qbic-pipelines/vcftomaf/pull/37) - Template update to 3.2.1 (@famosab)
 - [#38](https://github.com/qbic-pipelines/vcftomaf/pull/38) - Template update to 3.5.1 (@famosab)
+- [#39](https://github.com/qbic-pipelines/vcftomaf/pull/39) - Update all modules (@famosab)
 
 ### `Dependencies`
 
-| Dependency | Old version | New version |
-| ---------- | ----------- | ----------- |
-| MultiQC    | 1.25.1      | 1.32        |
+| Dependency.    | Old version | New version |
+| -------------- | ----------- | ----------- |
+| BCFtools       | 1.20        | 1.22        |
+| Gunzip         | 1.1         | 1.13        |
+| MultiQC        | 1.25.1      | 1.33        |
+| Picard         | 3.3.0       | 3.4.0       |
+| Tabix (HTSlib) | 1.20        | 1.21        |
 
 ### `Deprecated`
 
diff --git a/conf/base.config b/conf/base.config
index 333f3dc..986cb93 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -10,9 +10,9 @@
 
 process {
 
-    cpus   = { 1      * task.attempt }
-    memory = { 6.GB   * task.attempt }
-    time   = { 4.h    * task.attempt }
+    cpus          = { 1 * task.attempt }
+    memory        = { 6.GB * task.attempt }
+    time          = { 4.h * task.attempt }
 
     errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' }
     maxRetries    = 1
@@ -23,43 +23,43 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    withLabel:error_ignore {
+    withLabel: error_ignore {
         errorStrategy = 'ignore'
     }
-    withLabel:error_retry {
+    withLabel: error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withLabel:process_single {
-        cpus   = { 1                   }
+    withLabel: process_single {
+        cpus   = { 1 }
         memory = { 6.GB * task.attempt }
-        time   = { 4.h  * task.attempt }
+        time   = { 4.h * task.attempt }
     }
-    withLabel:process_low {
-        cpus   = { 2     * task.attempt }
+    withLabel: process_low {
+        cpus   = { 2 * task.attempt }
         memory = { 12.GB * task.attempt }
-        time   = { 4.h   * task.attempt }
+        time   = { 4.h * task.attempt }
     }
-    withLabel:process_medium {
-        cpus   = { 6     * task.attempt }
+    withLabel: process_medium {
+        cpus   = { 6 * task.attempt }
         memory = { 36.GB * task.attempt }
-        time   = { 8.h   * task.attempt }
+        time   = { 8.h * task.attempt }
     }
-    withLabel:process_high {
-        cpus   = { 12    * task.attempt }
+    withLabel: process_high {
+        cpus   = { 12 * task.attempt }
         memory = { 72.GB * task.attempt }
-        time   = { 16.h  * task.attempt }
+        time   = { 16.h * task.attempt }
     }
-    withLabel:process_long {
-        time   = { 20.h  * task.attempt }
+    withLabel: process_long {
+        time = { 20.h * task.attempt }
     }
-    withLabel:process_high_memory {
+    withLabel: process_high_memory {
         memory = { 200.GB * task.attempt }
     }
-    withLabel:error_ignore {
+    withLabel: error_ignore {
         errorStrategy = 'ignore'
     }
-    withLabel:error_retry {
+    withLabel: error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
diff --git a/conf/igenomes.config b/conf/igenomes.config
index 9f10cf6..2d5de1d 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -81,263 +81,263 @@ params {
             vep_version           = '108.2'
         }
         'Ensembl.GRCh37' {
-            bwa                   = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
-            snpeff_db             = 87
-            snpeff_genome         = 'GRCh37'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 108
-            vep_genome            = 'GRCh37'
-            vep_species           = 'homo_sapiens'
-            vep_version           = '108.2'
+            bwa               = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
+            readme            = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
+            snpeff_db         = 87
+            snpeff_genome     = 'GRCh37'
+            snpeff_version    = '5.1'
+            vep_cache_version = 108
+            vep_genome        = 'GRCh37'
+            vep_species       = 'homo_sapiens'
+            vep_version       = '108.2'
         }
         'NCBI.GRCh38' {
-            bwa                   = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
-            snpeff_db             = 105
-            snpeff_genome         = 'GRCh38'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 108
-            vep_genome            = 'GRCh38'
-            vep_species           = 'homo_sapiens'
-            vep_version           = '108.2'
-        }
-        'CHM13' {
-            fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
-            bwa                   = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
-            bwamem2               = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
-        }
-        'GRCm38' {
-            bwa                   = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
-            chr_dir               = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes"
-            dbsnp                 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
-            dbsnp_tbi             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
-            dict                  = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict"
-            fasta                 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
-            fasta_fai             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai"
-            intervals             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed"
-            known_indels          = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
-            known_indels_tbi      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
-            mappability           = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
-            readme                = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
-            snpeff_db             = 99
-            snpeff_genome         = 'GRCm38'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 102
-            vep_genome            = 'GRCm38'
-            vep_species           = 'mus_musculus'
-            vep_version           = '108.2'
-        }
-        'TAIR10' {
-            bwa                   = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
-        }
-        'EB2' {
-            bwa                   = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
+            bwa               = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
+            snpeff_db         = 105
+            snpeff_genome     = 'GRCh38'
+            snpeff_version    = '5.1'
+            vep_cache_version = 108
+            vep_genome        = 'GRCh38'
+            vep_species       = 'homo_sapiens'
+            vep_version       = '108.2'
+        }
+        CHM13 {
+            fasta   = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa"
+            bwa     = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/"
+            bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/"
+        }
+        GRCm38 {
+            bwa               = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/"
+            chr_dir           = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Chromosomes"
+            dbsnp             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz"
+            dbsnp_tbi         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.snps_all.dbSNP142.vcf.gz.tbi"
+            dict              = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.dict"
+            fasta             = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
+            fasta_fai         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai"
+            intervals         = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/intervals/GRCm38_calling_list.bed"
+            known_indels      = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz"
+            known_indels_tbi  = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/MouseGenomeProject/mgp.v5.merged.indels.dbSNP142.normed.vcf.gz.tbi"
+            mappability       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Control-FREEC/GRCm38_68_mm10.gem"
+            readme            = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
+            snpeff_db         = 99
+            snpeff_genome     = 'GRCm38'
+            snpeff_version    = '5.1'
+            vep_cache_version = 102
+            vep_genome        = 'GRCm38'
+            vep_species       = 'mus_musculus'
+            vep_version       = '108.2'
+        }
+        TAIR10 {
+            bwa    = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
+        }
+        EB2 {
+            bwa    = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
         }
         'UMD3.1' {
-            bwa                   = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
-            snpeff_db             = 75
-            snpeff_genome         = 'UMD3.1'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 94
-            vep_genome            = 'UMD3.1'
-            vep_species           = 'bos_taurus'
-            vep_version           = '108.2'
-        }
-        'WBcel235' {
-            bwa                   = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
-            snpeff_db             = 105
-            snpeff_genome         = 'WBcel235'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 108
-            vep_genome            = 'WBcel235'
-            vep_species           = 'caenorhabditis_elegans'
-            vep_version           = '108.2'
+            bwa               = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
+            readme            = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
+            snpeff_db         = 75
+            snpeff_genome     = 'UMD3.1'
+            snpeff_version    = '5.1'
+            vep_cache_version = 94
+            vep_genome        = 'UMD3.1'
+            vep_species       = 'bos_taurus'
+            vep_version       = '108.2'
+        }
+        WBcel235 {
+            bwa               = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
+            snpeff_db         = 105
+            snpeff_genome     = 'WBcel235'
+            snpeff_version    = '5.1'
+            vep_cache_version = 108
+            vep_genome        = 'WBcel235'
+            vep_species       = 'caenorhabditis_elegans'
+            vep_version       = '108.2'
         }
         'CanFam3.1' {
-            bwa                   = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
-            snpeff_db             = 99
-            snpeff_genome         = 'CanFam3.1'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 104
-            vep_genome            = 'CanFam3.1'
-            vep_species           = 'canis_lupus_familiaris'
-            vep_version           = '108.2'
-        }
-        'GRCz10' {
-            bwa                   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
-        }
-        'BDGP6' {
-            bwa                   = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
-        }
-        'EquCab2' {
-            bwa                   = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
-        }
-        'EB1' {
-            bwa                   = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
-        }
-        'Galgal4' {
-            bwa                   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
-        }
-        'Gm01' {
-            bwa                   = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
-        }
-        'Mmul_1' {
-            bwa                   = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
+            bwa               = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
+            readme            = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
+            snpeff_db         = 99
+            snpeff_genome     = 'CanFam3.1'
+            snpeff_version    = '5.1'
+            vep_cache_version = 104
+            vep_genome        = 'CanFam3.1'
+            vep_species       = 'canis_lupus_familiaris'
+            vep_version       = '108.2'
+        }
+        GRCz10 {
+            bwa   = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
+        }
+        BDGP6 {
+            bwa   = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
+        }
+        EquCab2 {
+            bwa    = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
+        }
+        EB1 {
+            bwa    = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
+        }
+        Galgal4 {
+            bwa   = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
+        }
+        Gm01 {
+            bwa    = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
+        }
+        Mmul_1 {
+            bwa    = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
         }
         'IRGSP-1.0' {
-            bwa                   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa   = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
         }
         'CHIMP2.1.4' {
-            bwa                   = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
+            bwa    = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
         }
         'Rnor_5.0' {
-            bwa                   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa"
         }
         'Rnor_6.0' {
-            bwa                   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
+            bwa   = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
         }
         'R64-1-1' {
-            bwa                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
-            snpeff_db             = 105
-            snpeff_genome         = 'R64-1-1'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 108
-            vep_genome            = 'R64-1-1'
-            vep_species           = 'saccharomyces_cerevisiae'
-            vep_version           = '108.2'
-        }
-        'EF2' {
-            bwa                   = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
-        }
-        'Sbi1' {
-            bwa                   = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
+            bwa               = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
+            snpeff_db         = 105
+            snpeff_genome     = 'R64-1-1'
+            snpeff_version    = '5.1'
+            vep_cache_version = 108
+            vep_genome        = 'R64-1-1'
+            vep_species       = 'saccharomyces_cerevisiae'
+            vep_version       = '108.2'
+        }
+        EF2 {
+            bwa    = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
+        }
+        Sbi1 {
+            bwa    = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
         }
         'Sscrofa10.2' {
-            bwa                   = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
-        }
-        'AGPv3' {
-            bwa                   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
-        }
-        'hg38' {
-            bwa                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
-            snpeff_db             = 105
-            snpeff_genome         = 'GRCh38'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 108
-            vep_genome            = 'GRCh38'
-            vep_species           = 'homo_sapiens'
-            vep_version           = '108.2'
-        }
-        'hg19' {
-            bwa                   = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
-            snpeff_db             = 87
-            snpeff_genome         = 'GRCh37'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 108
-            vep_genome            = 'GRCh37'
-            vep_species           = 'homo_sapiens'
-            vep_version           = '108.2'
-        }
-        'mm10' {
-            bwa                   = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
-            snpeff_db             = 99
-            snpeff_genome         = 'GRCm38'
-            snpeff_version        = '5.1'
-            vep_cache_version     = 102
-            vep_genome            = 'GRCm38'
-            vep_species           = 'mus_musculus'
-            vep_version           = '108.2'
-        }
-        'bosTau8' {
-            bwa                   = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
-        }
-        'ce10' {
-            bwa                   = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
-        }
-        'canFam3' {
-            bwa                   = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
-        }
-        'danRer10' {
-            bwa                   = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
-        }
-        'dm6' {
-            bwa                   = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
-        }
-        'equCab2' {
-            bwa                   = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
-        }
-        'galGal4' {
-            bwa                   = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
-        }
-        'panTro4' {
-            bwa                   = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
-        }
-        'rn6' {
-            bwa                   = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
-        }
-        'sacCer3' {
-            bwa                   = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
-        }
-        'susScr3' {
-            bwa                   = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
-            fasta                 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
-            readme                = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
+            bwa    = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
+        }
+        AGPv3 {
+            bwa   = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
+        }
+        hg38 {
+            bwa               = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
+            snpeff_db         = 105
+            snpeff_genome     = 'GRCh38'
+            snpeff_version    = '5.1'
+            vep_cache_version = 108
+            vep_genome        = 'GRCh38'
+            vep_species       = 'homo_sapiens'
+            vep_version       = '108.2'
+        }
+        hg19 {
+            bwa               = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
+            readme            = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
+            snpeff_db         = 87
+            snpeff_genome     = 'GRCh37'
+            snpeff_version    = '5.1'
+            vep_cache_version = 108
+            vep_genome        = 'GRCh37'
+            vep_species       = 'homo_sapiens'
+            vep_version       = '108.2'
+        }
+        mm10 {
+            bwa               = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/"
+            fasta             = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
+            readme            = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
+            snpeff_db         = 99
+            snpeff_genome     = 'GRCm38'
+            snpeff_version    = '5.1'
+            vep_cache_version = 102
+            vep_genome        = 'GRCm38'
+            vep_species       = 'mus_musculus'
+            vep_version       = '108.2'
+        }
+        bosTau8 {
+            bwa   = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
+        }
+        ce10 {
+            bwa    = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
+        }
+        canFam3 {
+            bwa    = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
+        }
+        danRer10 {
+            bwa   = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
+        }
+        dm6 {
+            bwa   = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
+        }
+        equCab2 {
+            bwa    = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
+        }
+        galGal4 {
+            bwa    = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
+        }
+        panTro4 {
+            bwa    = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
+        }
+        rn6 {
+            bwa   = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/"
+            fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
+        }
+        sacCer3 {
+            bwa    = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
+        }
+        susScr3 {
+            bwa    = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/"
+            fasta  = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
+            readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
         }
     }
 }
diff --git a/conf/modules.config b/conf/modules.config
index 49ad72d..f9e6dc1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -15,19 +15,21 @@ process {
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
     ]
 
     withName: BCFTOOLS_VIEW {
-        ext.args = { [ "",
-            params.filter ? "-f PASS": "",
-            "--output-type z"
-            ].join(" ").trim() }
+        ext.args = {
+            [
+                "",
+                params.filter ? "-f PASS" : "",
+                "--output-type z",
+            ].join(" ").trim()
+        }
     }
 
     withName: GUNZIP {
-        publishDir        = [
-            //specify to avoid publishing, overwritten otherwise
+        publishDir = [
             enabled: false
         ]
     }
@@ -37,61 +39,61 @@ process {
             [
                 path: { "${params.outdir}/liftover/lifted/" },
                 mode: params.publish_dir_mode,
-                pattern: "*.lifted.vcf.gz"
+                pattern: "*.lifted.vcf.gz",
             ],
             [
                 path: { "${params.outdir}/liftover/unlifted/" },
                 mode: params.publish_dir_mode,
-                pattern: "*.unlifted.vcf.gz"
+                pattern: "*.unlifted.vcf.gz",
             ],
             [
                 path: { "${params.outdir}/liftover/logs/" },
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
-            ]
+                pattern: "*.log",
+            ],
         ]
     }
 
     withName: TABIX_TABIX {
-        publishDir        = [
-            //specify to avoid publishing, overwritten otherwise
+        publishDir = [
             enabled: false
         ]
     }
 
     withName: UNTAR {
-        publishDir        = [
-            //specify to avoid publishing, overwritten otherwise
+        publishDir = [
             enabled: false
         ]
     }
 
     withName: VCF2MAF {
-        ext.args = { [ "",
-            params.run_vep ? "" : "--inhibit-vep",
-            meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
-            meta.tumor_id  ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}"     : "",
-            "--retain-fmt AD,AF,DP,GQ,GT,STR",
-            "--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
-            "--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
-            "--any-allele",
-            "--ncbi-build ${params.genome.tokenize('.')[-1]}",
-            "--species homo_sapiens"
-        ].join(" ").trim() }
+        ext.args   = {
+            [
+                "",
+                params.run_vep ? "" : "--inhibit-vep",
+                meta.normal_id ? "--normal-id ${meta.normal_id} --vcf-normal-id ${meta.vcf_normal_id}" : "",
+                meta.tumor_id ? "--tumor-id ${meta.tumor_id} --vcf-tumor-id ${meta.vcf_tumor_id}" : "",
+                "--retain-fmt AD,AF,DP,GQ,GT,STR",
+                "--retain-info AS_FilterStatus,AS_SB_TABLE,DP,MBQ,POPAF,STR,ANN,LOF,NMD",
+                "--retain-ann Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,CDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,MANE_SELECT,MANE_PLUS_CLINICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,UNIPROT_ISOFORM,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,gnomADe_AF,gnomADe_AFR_AF,gnomADe_AMR_AF,gnomADe_ASJ_AF,gnomADe_EAS_AF,gnomADe_FIN_AF,gnomADe_MID_AF,gnomADe_NFE_AF,gnomADe_REMAINING_AF,gnomADe_SAS_AF,gnomADg_AF,gnomADg_AFR_AF,gnomADg_AMI_AF,gnomADg_AMR_AF,gnomADg_ASJ_AFIgnomADg_EAS_AF,gnomADg_FIN_AF,gnomADg_MID_AF,gnomADg_NFE_AF,gnomADg_REMAINING_AF,gnomADg_SAS_AF,gnomADg_EAS_AF_POPS,FREQS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE,TRANSCRIPTION_FACTORS",
+                "--any-allele",
+                "--ncbi-build ${params.genome.tokenize('.')[-1]}",
+                "--species homo_sapiens",
+            ].join(" ").trim()
+        }
         publishDir = [
             path: { "${params.outdir}/maf" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
-    withName: 'MULTIQC' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+    withName: MULTIQC {
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
-
 }
diff --git a/conf/test.config b/conf/test.config
index 7e254f2..3703a4d 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -14,7 +14,7 @@ process {
     resourceLimits = [
         cpus: 4,
         memory: '15.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 }
 
@@ -23,10 +23,9 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    input        = "${projectDir}/tests/samplesheets/samplesheet.csv"
-    fasta        = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
-    intervals    = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
-    genome       = 'GATK.GRCh38'
-    filter       = false
-
+    input                      = "${projectDir}/tests/samplesheets/samplesheet.csv"
+    fasta                      = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    intervals                  = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.bed'
+    genome                     = 'GATK.GRCh38'
+    filter                     = false
 }
diff --git a/main.nf b/main.nf
index c32d5a6..2702b9c 100644
--- a/main.nf
+++ b/main.nf
@@ -17,6 +17,46 @@ include { VCFTOMAF                } from './workflows/vcftomaf'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_vcftomaf_pipeline'
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    RUN MAIN WORKFLOW
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow {
+    //
+    // SUBWORKFLOW: Run initialisation tasks
+    //
+    PIPELINE_INITIALISATION(
+        params.version,
+        params.validate_params,
+        params.monochrome_logs,
+        args,
+        params.outdir,
+        params.input,
+        params.help,
+        params.help_full,
+        params.show_hidden,
+    )
+
+    //
+    // WORKFLOW: Run main workflow
+    //
+    QBICPIPELINES_VCFTOMAF(
+        PIPELINE_INITIALISATION.out.samplesheet
+    )
+
+    //
+    PIPELINE_COMPLETION(
+        params.email,
+        params.email_on_fail,
+        params.plaintext_email,
+        params.outdir,
+        params.monochrome_logs,
+        params.hook_url,
+        QBICPIPELINES_VCFTOMAF.out.multiqc_report,
+    )
+}
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -28,12 +68,10 @@ include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_vcft
 // WORKFLOW: Run main analysis pipeline depending on type of input
 //
 workflow QBICPIPELINES_VCFTOMAF {
-
     take:
     samplesheet // channel: samplesheet read in from --input
 
     main:
-
     //
     // SET PARAMETERS
     //
@@ -41,84 +79,31 @@ workflow QBICPIPELINES_VCFTOMAF {
     params.dict = getGenomeAttribute('dict')
 
     // Extra files
-    intervals      = params.intervals      ? Channel.fromPath(params.intervals).collect()      : Channel.value([])
-    liftover_chain = params.liftover_chain ? Channel.fromPath(params.liftover_chain).collect() : Channel.value([])
+    intervals = params.intervals ? channel.fromPath(params.intervals).collect() : channel.value([])
+    liftover_chain = params.liftover_chain ? channel.fromPath(params.liftover_chain).collect() : channel.value([])
 
     // FASTA
-    fasta        = params.fasta     ? Channel.fromPath(params.fasta).collect()          : Channel.value([])
-    dict         = params.dict      ? Channel.fromPath(params.dict).collect()           : Channel.empty()
-
-    // Genome version
-    genome        = params.genome   ?: Channel.empty()
+    fasta = params.fasta ? channel.fromPath(params.fasta).collect() : channel.value([])
+    dict = params.dict ? channel.fromPath(params.dict).collect() : channel.empty()
 
     // VEP cache
-    vep_cache          = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : Channel.value([])
-    vep_cache_unpacked = Channel.value([])
-
+    vep_cache = params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([])
+    vep_cache_unpacked = channel.value([])
 
     //
     // WORKFLOW: Run pipeline
     //
 
-    VCFTOMAF (
+    VCFTOMAF(
         samplesheet,
         intervals,
         fasta,
         dict,
         liftover_chain,
-        genome,
         vep_cache,
-        vep_cache_unpacked
+        vep_cache_unpacked,
     )
 
     emit:
     multiqc_report = VCFTOMAF.out.multiqc_report // channel: /path/to/multiqc_report.html
 }
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN MAIN WORKFLOW
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow {
-
-    main:
-    //
-    // SUBWORKFLOW: Run initialisation tasks
-    //
-    PIPELINE_INITIALISATION (
-        params.version,
-        params.validate_params,
-        params.monochrome_logs,
-        args,
-        params.outdir,
-        params.input,
-        params.help,
-        params.help_full,
-        params.show_hidden
-    )
-
-    //
-    // WORKFLOW: Run main workflow
-    //
-    QBICPIPELINES_VCFTOMAF (
-        PIPELINE_INITIALISATION.out.samplesheet
-    )
-
-    //
-    PIPELINE_COMPLETION (
-        params.email,
-        params.email_on_fail,
-        params.plaintext_email,
-        params.outdir,
-        params.monochrome_logs,
-        params.hook_url,
-        QBICPIPELINES_VCFTOMAF.out.multiqc_report
-    )
-}
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
diff --git a/modules.json b/modules.json
index 925fac8..83e3e75 100644
--- a/modules.json
+++ b/modules.json
@@ -7,37 +7,37 @@
                 "nf-core": {
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "dfa7f1a33781e89f6efe727d371ed7ca9077059d",
+                        "git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
                         "installed_by": ["modules"]
                     },
                     "picard/liftovervcf": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "7b972bdde6fa2154a95cf08a8ba1821f228f20d3",
+                        "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408",
                         "installed_by": ["modules"]
                     },
                     "vcf2maf": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml
index 5c00b11..ba863b3 100644
--- a/modules/nf-core/bcftools/view/environment.yml
+++ b/modules/nf-core/bcftools/view/environment.yml
@@ -1,5 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::bcftools=1.20
+  # renovate: datasource=conda depName=bioconda/htslib
+  - bioconda::htslib=1.22.1
+  # renovate: datasource=conda depName=bioconda/bcftools
+  - bioconda::bcftools=1.22
diff --git a/modules/nf-core/bcftools/view/main.nf b/modules/nf-core/bcftools/view/main.nf
index 7fe4303..72b3120 100644
--- a/modules/nf-core/bcftools/view/main.nf
+++ b/modules/nf-core/bcftools/view/main.nf
@@ -4,8 +4,8 @@ process BCFTOOLS_VIEW {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
-        'biocontainers/bcftools:1.20--h8b25389_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data':
+        'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
@@ -57,13 +57,12 @@ process BCFTOOLS_VIEW {
                     args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                     args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
                     "vcf"
-    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
-                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
-                args.contains("--write-index") || args.contains("-W") ? "csi" :
-                ""
+    def stub_index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
+                     args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
+                     args.contains("--write-index")     || args.contains("-W") ? "csi" :
+                     ""
     def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
-    def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : ""
-
+    def create_index = extension.endsWith(".gz") && stub_index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${stub_index}" : ""
     """
     ${create_cmd} ${prefix}.${extension}
     ${create_index}
diff --git a/modules/nf-core/bcftools/view/meta.yml b/modules/nf-core/bcftools/view/meta.yml
index aa7785f..e9df974 100644
--- a/modules/nf-core/bcftools/view/meta.yml
+++ b/modules/nf-core/bcftools/view/meta.yml
@@ -26,29 +26,34 @@ input:
         description: |
           The vcf file to be inspected.
           e.g. 'file.vcf'
+        ontologies: []
     - index:
         type: file
         description: |
           The tab index for the VCF file to be inspected.
           e.g. 'file.tbi'
-  - - regions:
-        type: file
-        description: |
-          Optionally, restrict the operation to regions listed in this file.
-          e.g. 'file.vcf'
-  - - targets:
-        type: file
-        description: |
-          Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
-          e.g. 'file.vcf'
-  - - samples:
-        type: file
-        description: |
-          Optional, file of sample names to be included or excluded.
-          e.g. 'file.tsv'
+        ontologies: []
+  - regions:
+      type: file
+      description: |
+        Optionally, restrict the operation to regions listed in this file.
+        e.g. 'file.vcf'
+      ontologies: []
+  - targets:
+      type: file
+      description: |
+        Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
+        e.g. 'file.vcf'
+      ontologies: []
+  - samples:
+      type: file
+      description: |
+        Optional, file of sample names to be included or excluded.
+        e.g. 'file.tsv'
+      ontologies: []
 output:
-  - vcf:
-      - meta:
+  vcf:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -57,8 +62,9 @@ output:
           type: file
           description: VCF normalized output file
           pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
-  - tbi:
-      - meta:
+          ontologies: []
+  tbi:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -67,8 +73,9 @@ output:
           type: file
           description: Alternative VCF file index
           pattern: "*.tbi"
-  - csi:
-      - meta:
+          ontologies: []
+  csi:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -77,11 +84,14 @@ output:
           type: file
           description: Default VCF file index
           pattern: "*.csi"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@abhi18av"
 maintainers:
diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test b/modules/nf-core/bcftools/view/tests/main.nf.test
index 1e60c50..8281c17 100644
--- a/modules/nf-core/bcftools/view/tests/main.nf.test
+++ b/modules/nf-core/bcftools/view/tests/main.nf.test
@@ -295,4 +295,4 @@ nextflow_process {
 
     }
 
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bcftools/view/tests/main.nf.test.snap b/modules/nf-core/bcftools/view/tests/main.nf.test.snap
index fec22e3..38b61e4 100644
--- a/modules/nf-core/bcftools/view/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/view/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
                 ],
                 "csi": [
                     [
@@ -48,15 +48,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-06-05T12:14:38.717458272"
+        "timestamp": "2025-09-11T14:59:19.949819"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": {
         "content": [
@@ -82,14 +82,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-06-05T12:13:44.760671384"
+        "timestamp": "2025-09-11T14:59:00.329884"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": {
         "content": [
@@ -116,7 +116,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
                 ],
                 "csi": [
                     [
@@ -140,15 +140,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-06-04T16:06:21.669668533"
+        "timestamp": "2025-09-11T14:59:15.546282"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": {
         "content": [
@@ -175,7 +175,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
                 ],
                 "csi": [
                     
@@ -199,15 +199,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                    "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-06-05T12:14:53.026083914"
+        "timestamp": "2025-09-11T14:59:24.406961"
     },
     "sarscov2 - [vcf, tbi], vcf, tsv, []": {
         "content": [
@@ -221,27 +221,27 @@
                 ]
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-05-31T15:15:14.663512924"
+        "timestamp": "2025-09-11T14:59:05.680096"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - stub": {
         "content": [
             "out.vcf",
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-05-31T15:15:19.723448323"
+        "timestamp": "2025-09-11T14:59:10.959586"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": {
         "content": [
@@ -267,14 +267,14 @@
                 
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-06-05T08:24:36.358469315"
+        "timestamp": "2025-09-11T14:58:50.932203"
     },
     "sarscov2 - [vcf, tbi], [], [], []": {
         "content": [
@@ -288,14 +288,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-05-31T15:15:09.588867653"
+        "timestamp": "2025-09-11T14:58:45.877214"
     },
     "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": {
         "content": [
@@ -321,13 +321,13 @@
                 
             ],
             [
-                "versions.yml:md5,241125d00357804552689c37bbabe1f5"
+                "versions.yml:md5,ad4e3c17561ccfd75a5438895b687d60"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-06-05T12:13:33.834986869"
+        "timestamp": "2025-09-11T14:58:55.616644"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/view/tests/tags.yml b/modules/nf-core/bcftools/view/tests/tags.yml
deleted file mode 100644
index 43b1f0a..0000000
--- a/modules/nf-core/bcftools/view/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-bcftools/view:
-  - "modules/nf-core/bcftools/view/**"
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
index c779485..9b926b1 100644
--- a/modules/nf-core/gunzip/environment.yml
+++ b/modules/nf-core/gunzip/environment.yml
@@ -1,7 +1,12 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
+  - conda-forge::coreutils=9.5
   - conda-forge::grep=3.11
+  - conda-forge::gzip=1.13
+  - conda-forge::lbzip2=2.5
   - conda-forge::sed=4.8
   - conda-forge::tar=1.34
diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf
index 5e67e3b..3ffc8e9 100644
--- a/modules/nf-core/gunzip/main.nf
+++ b/modules/nf-core/gunzip/main.nf
@@ -1,37 +1,37 @@
 process GUNZIP {
-    tag "$archive"
+    tag "${archive}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
-        'nf-core/ubuntu:22.04' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
+        : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
 
     input:
     tuple val(meta), path(archive)
 
     output:
-    tuple val(meta), path("$gunzip"), emit: gunzip
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path("${gunzip}"), emit: gunzip
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args        = task.ext.args ?: ''
-    def extension   = ( archive.toString() - '.gz' ).tokenize('.')[-1]
-    def name        = archive.toString() - '.gz' - ".$extension"
-    def prefix      = task.ext.prefix ?: name
-    gunzip          = prefix + ".$extension"
+    def args = task.ext.args ?: ''
+    def extension = (archive.toString() - '.gz').tokenize('.')[-1]
+    def name = archive.toString() - '.gz' - ".${extension}"
+    def prefix = task.ext.prefix ?: name
+    gunzip = prefix + ".${extension}"
     """
     # Not calling gunzip itself because it creates files
     # with the original group ownership rather than the
     # default one for that user / the work directory
     gzip \\
         -cd \\
-        $args \\
-        $archive \\
-        > $gunzip
+        ${args} \\
+        ${archive} \\
+        > ${gunzip}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -40,13 +40,13 @@ process GUNZIP {
     """
 
     stub:
-    def args        = task.ext.args ?: ''
-    def extension   = ( archive.toString() - '.gz' ).tokenize('.')[-1]
-    def name        = archive.toString() - '.gz' - ".$extension"
-    def prefix      = task.ext.prefix ?: name
-    gunzip          = prefix + ".$extension"
+    def args = task.ext.args ?: ''
+    def extension = (archive.toString() - '.gz').tokenize('.')[-1]
+    def name = archive.toString() - '.gz' - ".${extension}"
+    def prefix = task.ext.prefix ?: name
+    gunzip = prefix + ".${extension}"
     """
-    touch $gunzip
+    touch ${gunzip}
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml
index 9066c03..926bb22 100644
--- a/modules/nf-core/gunzip/meta.yml
+++ b/modules/nf-core/gunzip/meta.yml
@@ -21,21 +21,26 @@ input:
         type: file
         description: File to be compressed/uncompressed
         pattern: "*.*"
+        ontologies: []
 output:
-  - gunzip:
-      - meta:
+  gunzip:
+    - - meta:
           type: file
           description: Compressed/uncompressed file
           pattern: "*.*"
-      - $gunzip:
+          ontologies: []
+      - ${gunzip}:
           type: file
           description: Compressed/uncompressed file
           pattern: "*.*"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap
index 069967e..a0f0e67 100644
--- a/modules/nf-core/gunzip/tests/main.nf.test.snap
+++ b/modules/nf-core/gunzip/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                    "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c"
                 ],
                 "gunzip": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                    "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-06-25T11:35:10.861293"
+        "timestamp": "2024-12-13T11:48:22.080222697"
     },
     "Should run without failures - stub": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                    "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c"
                 ],
                 "gunzip": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                    "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-06-25T11:35:05.857145"
+        "timestamp": "2024-12-13T11:48:14.593020264"
     },
     "Should run without failures": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                    "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c"
                 ],
                 "gunzip": [
                     [
@@ -88,15 +88,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                    "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2023-10-17T15:35:37.690477896"
+        "timestamp": "2024-12-13T11:48:01.295397925"
     },
     "Should run without failures - prefix": {
         "content": [
@@ -110,7 +110,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                    "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c"
                 ],
                 "gunzip": [
                     [
@@ -121,14 +121,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,54376d32aca20e937a4ec26dac228e84"
+                    "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-06-25T11:33:32.921739"
+        "timestamp": "2024-12-13T11:48:07.414271387"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml
deleted file mode 100644
index fd3f691..0000000
--- a/modules/nf-core/gunzip/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-gunzip:
-  - modules/nf-core/gunzip/**
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index d02016a..009874d 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.32
+  - bioconda::multiqc=1.33
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 82f8979..3b0e975 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
-        'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' :
+        'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b' }"
 
     input:
     path multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 3a8ce6b..d72d35b 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -6,14 +6,14 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.32"
+                        "1.33"
                     ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
         "timestamp": "2025-12-09T10:10:43.020315838"
     },
@@ -28,15 +28,15 @@
                         [
                             "MULTIQC",
                             "multiqc",
-                            "1.32"
+                            "1.33"
                         ]
                     ]
                 }
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
         "timestamp": "2025-12-09T10:11:14.131950776"
     },
@@ -47,14 +47,14 @@
                     [
                         "MULTIQC",
                         "multiqc",
-                        "1.32"
+                        "1.33"
                     ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
         "timestamp": "2025-12-09T10:11:07.15692209"
     }
diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml
index fb68506..b4ac4fe 100644
--- a/modules/nf-core/picard/liftovervcf/environment.yml
+++ b/modules/nf-core/picard/liftovervcf/environment.yml
@@ -1,5 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::picard=3.3.0
\ No newline at end of file
+  # renovate: datasource=conda depName=bioconda/picard
+  - bioconda::picard=3.4.0
diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf
index 69feb62..b38f297 100644
--- a/modules/nf-core/picard/liftovervcf/main.nf
+++ b/modules/nf-core/picard/liftovervcf/main.nf
@@ -4,8 +4,8 @@ process PICARD_LIFTOVERVCF {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
-        'biocontainers/picard:3.3.0--hdfd78af_0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/08/0861295baa7c01fc593a9da94e82b44a729dcaf8da92be8e565da109aa549b25/data' :
+        'community.wave.seqera.io/library/picard:3.4.0--e9963040df0a9bf6' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/picard/liftovervcf/meta.yml b/modules/nf-core/picard/liftovervcf/meta.yml
index 10fbfc8..79baa3c 100644
--- a/modules/nf-core/picard/liftovervcf/meta.yml
+++ b/modules/nf-core/picard/liftovervcf/meta.yml
@@ -21,6 +21,7 @@ input:
         type: file
         description: VCF file
         pattern: "*.{vcf,vcf.gz}"
+        ontologies: []
   - - meta2:
         type: map
         description: |
@@ -30,6 +31,7 @@ input:
         type: file
         description: dictionary for fasta file
         pattern: "*.{dict}"
+        ontologies: []
   - - meta3:
         type: map
         description: |
@@ -39,6 +41,7 @@ input:
         type: file
         description: fasta file
         pattern: "*.fasta"
+        ontologies: []
   - - meta4:
         type: map
         description: |
@@ -47,9 +50,10 @@ input:
     - chain:
         type: file
         description: The liftover chain file
+        ontologies: []
 output:
-  - vcf_lifted:
-      - meta:
+  vcf_lifted:
+    - - meta:
           type: map
           description: Groovy Map containing sample information e.g. [ id:'test', single_end:false
             ]
@@ -57,8 +61,9 @@ output:
           type: file
           description: VCF file containing successfully lifted variants
           pattern: "*.{lifted.vcf.gz}"
-  - vcf_unlifted:
-      - meta:
+          ontologies: []
+  vcf_unlifted:
+    - - meta:
           type: map
           description: Groovy Map containing sample information e.g. [ id:'test', single_end:false
             ]
@@ -66,11 +71,14 @@ output:
           type: file
           description: VCF file containing unsuccessfully lifted variants
           pattern: "*.{unlifted.vcf.gz}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@lucpen"
   - "@ramprasadn"
diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap
index e88aa97..4a2185e 100644
--- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap
+++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap
@@ -4,27 +4,27 @@
             "test.lifted.vcf.gz",
             "test.unlifted.vcf.gz",
             [
-                "versions.yml:md5,af33ca5d76aec86863614805fbb4fafb"
+                "versions.yml:md5,c7ca1d1d7479af5c94b33259bc383383"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-10-18T12:08:23.913395641"
+        "timestamp": "2025-09-15T10:53:49.795435027"
     },
     "test-picard-liftovervcf": {
         "content": [
             "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]",
             "39a9de5185d94289283bd27cfcdeba97",
             [
-                "versions.yml:md5,af33ca5d76aec86863614805fbb4fafb"
+                "versions.yml:md5,c7ca1d1d7479af5c94b33259bc383383"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-10-18T12:08:12.803193917"
+        "timestamp": "2025-09-15T10:53:40.572212144"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml
index 017c259..771b138 100644
--- a/modules/nf-core/tabix/tabix/environment.yml
+++ b/modules/nf-core/tabix/tabix/environment.yml
@@ -1,7 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 
 dependencies:
-  - bioconda::htslib=1.20
-  - bioconda::tabix=1.11
+  - bioconda::htslib=1.21
diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 13acd67..602a82a 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -4,16 +4,15 @@ process TABIX_TABIX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' :
-        'biocontainers/htslib:1.20--h5efdd21_2' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd/data' :
+        'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
 
     input:
     tuple val(meta), path(tab)
 
     output:
-    tuple val(meta), path("*.tbi"), optional:true, emit: tbi
-    tuple val(meta), path("*.csi"), optional:true, emit: csi
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.{tbi,csi}"), emit: index
+    tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'")   , topic: versions   , emit: versions_tabix
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,20 +25,12 @@ process TABIX_TABIX {
         $args \\
         $tab
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
     """
-
     stub:
+    def args = task.ext.args ?: ''
+    def index = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
     """
     touch ${tab}.tbi
     touch ${tab}.csi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index 7864832..f5b6b3c 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -22,32 +22,42 @@ input:
         type: file
         description: TAB-delimited genome position file compressed with bgzip
         pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
+        ontologies: []
 output:
-  - tbi:
-      - meta:
+  index:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.tbi":
+      - "*.{tbi,csi}":
           type: file
-          description: tabix index file
-          pattern: "*.{tbi}"
-  - csi:
-      - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.csi":
-          type: file
-          description: coordinate sorted index file
-          pattern: "*.{csi}"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          description: Tabix index file (either tbi or csi)
+          pattern: "*.{tbi,csi}"
+          ontologies: []
+  versions_tabix:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - tabix:
+          type: string
+          description: The tool name
+      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - tabix:
+          type: string
+          description: The tool name
+      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 102b0d7..19eefab 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -1,7 +1,7 @@
 nextflow_process {
 
     name "Test Process TABIX_TABIX"
-    script "modules/nf-core/tabix/tabix/main.nf"
+    script "../main.nf"
     process "TABIX_TABIX"
 
     tag "modules"
@@ -9,9 +9,13 @@ nextflow_process {
     tag "tabix"
     tag "tabix/tabix"
 
+    config "./nextflow.config"
+
     test("sarscov2_bedgz_tbi") {
-        config "./tabix_bed.config"
         when {
+            params {
+                module_args = '-p bed'
+            }
             process {
                 """
                 input[0] = [
@@ -25,17 +29,16 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    file(process.out.tbi[0][1]).name
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
     test("sarscov2_gff_tbi") {
-        config "./tabix_gff.config"
         when {
+            params {
+                module_args = '-p gff'
+            }
             process {
                 """
                 input[0] = [
@@ -49,17 +52,17 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    file(process.out.tbi[0][1]).name).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
     }
 
     test("sarscov2_vcf_tbi") {
-        config "./tabix_vcf_tbi.config"
         when {
+            params {
+                module_args = '-p vcf'
+            }
             process {
                 """
                 input[0] =  [
@@ -73,18 +76,17 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    file(process.out.tbi[0][1]).name
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
     }
 
     test("sarscov2_vcf_csi") {
-        config "./tabix_vcf_csi.config"
         when {
+            params {
+                module_args = '-p vcf --csi'
+            }
             process {
                 """
                 input[0] =  [
@@ -98,19 +100,18 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    file(process.out.csi[0][1]).name
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
     }
 
     test("sarscov2_vcf_csi_stub") {
-        config "./tabix_vcf_csi.config"
         options "-stub"
         when {
+            params {
+                module_args = '-p vcf --csi'
+            }
             process {
                 """
                 input[0] =  [
@@ -124,13 +125,9 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    file(process.out.csi[0][1]).name
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
-
     }
 
 }
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
index c2b9ed0..7e4c1ee 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -11,15 +11,13 @@
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
-                ],
-                "csi": [
-                    
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
-                "tbi": [
+                "index": [
                     [
                         {
                             "id": "tbi_gff"
@@ -27,17 +25,20 @@
                         "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
-            },
-            "genome.gff3.gz.tbi"
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-07-19T12:06:25.653807564"
+        "timestamp": "2025-11-20T13:47:34.055936"
     },
     "sarscov2_bedgz_tbi": {
         "content": [
@@ -51,15 +52,13 @@
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
-                ],
-                "csi": [
-                    
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
-                "tbi": [
+                "index": [
                     [
                         {
                             "id": "tbi_bed"
@@ -67,17 +66,20 @@
                         "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
-            },
-            "test.bed.gz.tbi"
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-07-19T12:06:09.754082161"
+        "timestamp": "2025-11-20T13:47:29.90469"
     },
     "sarscov2_vcf_tbi": {
         "content": [
@@ -91,15 +93,13 @@
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
-                ],
-                "csi": [
-                    
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
-                "tbi": [
+                "index": [
                     [
                         {
                             "id": "tbi_vcf"
@@ -107,17 +107,20 @@
                         "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
-            },
-            "test.vcf.gz.tbi"
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-07-19T12:06:40.042648294"
+        "timestamp": "2025-11-20T13:47:38.044307"
     },
     "sarscov2_vcf_csi_stub": {
         "content": [
@@ -127,55 +130,49 @@
                         {
                             "id": "vcf_csi_stub"
                         },
-                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "1": [
                     [
-                        {
-                            "id": "vcf_csi_stub"
-                        },
-                        "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
                     ]
                 ],
-                "2": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
-                ],
-                "csi": [
+                "index": [
                     [
                         {
                             "id": "vcf_csi_stub"
                         },
-                        "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        [
+                            "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
-                "tbi": [
+                "versions_tabix": [
                     [
-                        {
-                            "id": "vcf_csi_stub"
-                        },
-                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
                 ]
-            },
-            "test.vcf.gz.csi"
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-07-19T12:07:08.700367261"
+        "timestamp": "2025-11-20T13:47:46.12436"
     },
     "sarscov2_vcf_csi": {
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     [
                         {
                             "id": "vcf_csi"
@@ -183,10 +180,14 @@
                         "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b"
                     ]
                 ],
-                "2": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                "1": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
-                "csi": [
+                "index": [
                     [
                         {
                             "id": "vcf_csi"
@@ -194,19 +195,19 @@
                         "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b"
                     ]
                 ],
-                "tbi": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,07064637fb8a217174052be8e40234e2"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
-            },
-            "test.vcf.gz.csi"
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-07-19T12:06:55.362067748"
+        "timestamp": "2025-11-20T13:47:42.013054"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config
deleted file mode 100644
index 7ff0590..0000000
--- a/modules/nf-core/tabix/tabix/tests/tabix_bed.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: TABIX_TABIX {
-        ext.args = '-p bed'
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config
deleted file mode 100644
index 20c0a1e..0000000
--- a/modules/nf-core/tabix/tabix/tests/tabix_gff.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: TABIX_TABIX {
-        ext.args = '-p gff'
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config
deleted file mode 100644
index eb4f2d7..0000000
--- a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: TABIX_TABIX {
-        ext.args = '-p vcf --csi'
-    }
-}
diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config
deleted file mode 100644
index 2774c8a..0000000
--- a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: TABIX_TABIX {
-        ext.args = '-p vcf'
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml
deleted file mode 100644
index 6eda065..0000000
--- a/modules/nf-core/tabix/tabix/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-tabix/tabix:
-  - "modules/nf-core/tabix/tabix/**"
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
index ae4fa45..9b926b1 100644
--- a/modules/nf-core/untar/environment.yml
+++ b/modules/nf-core/untar/environment.yml
@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml
index 3a37bb3..1603e38 100644
--- a/modules/nf-core/untar/meta.yml
+++ b/modules/nf-core/untar/meta.yml
@@ -1,5 +1,5 @@
 name: untar
-description: Extract files.
+description: Extract files from tar, tar.gz, tar.bz2, tar.xz archives
 keywords:
   - untar
   - uncompress
@@ -7,7 +7,7 @@ keywords:
 tools:
   - untar:
       description: |
-        Extract tar.gz files.
+        Extract tar, tar.gz, tar.bz2, tar.xz files.
       documentation: https://www.gnu.org/software/tar/manual/
       licence: ["GPL-3.0-or-later"]
       identifier: ""
@@ -19,11 +19,14 @@ input:
           e.g. [ id:'test', single_end:false ]
     - archive:
         type: file
-        description: File to be untar
-        pattern: "*.{tar}.{gz}"
+        description: File to be untarred
+        pattern: "*.{tar,tar.gz,tar.bz2,tar.xz}"
+        ontologies:
+          - edam: http://edamontology.org/format_3981 # TAR format
+          - edam: http://edamontology.org/format_3989 # GZIP format
 output:
-  - untar:
-      - meta:
+  untar:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -35,11 +38,13 @@ output:
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
           pattern: "*/"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml
deleted file mode 100644
index feb6f15..0000000
--- a/modules/nf-core/untar/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-untar:
-  - modules/nf-core/untar/**
diff --git a/modules/nf-core/vcf2maf/environment.yml b/modules/nf-core/vcf2maf/environment.yml
index b5b73f4..4e617a0 100644
--- a/modules/nf-core/vcf2maf/environment.yml
+++ b/modules/nf-core/vcf2maf/environment.yml
@@ -1,3 +1,5 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/vcf2maf/meta.yml b/modules/nf-core/vcf2maf/meta.yml
index e5ce083..a1a0512 100644
--- a/modules/nf-core/vcf2maf/meta.yml
+++ b/modules/nf-core/vcf2maf/meta.yml
@@ -24,17 +24,20 @@ input:
         type: file
         description: |
           vcf to convert to MAF format. Must be uncompressed.
-  - - fasta:
-        type: file
-        description: |
-          Path to reference genome fasta file.
-  - - vep_cache:
-        type: file
-        description: |
-          Path to VEP cache dir. Required for correct running of VEP.
+        ontologies: []
+  - fasta:
+      type: file
+      description: |
+        Path to reference genome fasta file.
+      ontologies: []
+  - vep_cache:
+      type: file
+      description: |
+        Path to VEP cache dir. Required for correct running of VEP.
+      ontologies: []
 output:
-  - maf:
-      - meta:
+  maf:
+    - - meta:
           type: map
           description: |
             Groovy Map containing sample information
@@ -43,11 +46,14 @@ output:
           type: file
           description: MAF file produced from VCF
           pattern: "*.maf"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@adamrtalbot"
 maintainers:
diff --git a/modules/nf-core/vcf2maf/vcf2maf.diff b/modules/nf-core/vcf2maf/vcf2maf.diff
deleted file mode 100644
index 8442adc..0000000
--- a/modules/nf-core/vcf2maf/vcf2maf.diff
+++ /dev/null
@@ -1,51 +0,0 @@
-Changes in module 'nf-core/vcf2maf'
---- modules/nf-core/vcf2maf/environment.yml
-+++ modules/nf-core/vcf2maf/environment.yml
-@@ -5,4 +5,4 @@
-   - defaults
- dependencies:
-   - bioconda::vcf2maf=1.6.21
--  - bioconda::ensembl-vep=106.1
-+  - bioconda::ensembl-vep=108.2
-
---- modules/nf-core/vcf2maf/main.nf
-+++ modules/nf-core/vcf2maf/main.nf
-@@ -6,12 +6,13 @@
-     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-     conda "${moduleDir}/environment.yml"
-     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
--        'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0':
--        'biocontainers/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0' }"
-+        'https://depot.galaxyproject.org/singularity/mulled-v2-b1882a8fe50273c1485ae9ededaf10b625862cc1:2e14951bfa86df1bc30bb0dc1a0a3ec5fbaa5fd2-0':
-+        'biocontainers/mulled-v2-b1882a8fe50273c1485ae9ededaf10b625862cc1:2e14951bfa86df1bc30bb0dc1a0a3ec5fbaa5fd2-0' }"
- 
-     input:
-     tuple val(meta), path(vcf) // Use an uncompressed VCF file!
-     path fasta                 // Required
-+    val genome                 // Required
-     path vep_cache             // Required for VEP running. A default of /.vep is supplied.
- 
-     output:
-@@ -25,9 +26,11 @@
-     def args          = task.ext.args   ?: ''
-     def prefix        = task.ext.prefix ?: "${meta.id}"
-     def vep_cache_cmd = vep_cache       ? "--vep-data $vep_cache" : ""
-+    def genome_build  = genome          ? "--ncbi-build $genome"  : ""
-+
-     // If VEP is present, it will find it and add it to commands.
-     // If VEP is not present they will be blank
--    def VERSION = '1.6.21' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-+    def VERSION = '1.6.21.20230511' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-     """
-     if command -v vep &> /dev/null
-     then
-@@ -42,6 +45,7 @@
-         $args \\
-         \$VEP_CMD \\
-         $vep_cache_cmd \\
-+        $genome_build \\
-         --ref-fasta $fasta \\
-         --input-vcf $vcf \\
-         --output-maf ${prefix}.maf
-
-************************************************************
diff --git a/nextflow.config b/nextflow.config
index 8ab40c0..de4bd92 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,24 +10,24 @@
 params {
 
     // Input options
-    liftover_chain             = null
-    input                      = null
-    intervals                  = null
-    vep_cache                  = null
-    run_vep                    = false
-    filter                     = false
+    liftover_chain               = null
+    input                        = null
+    intervals                    = null
+    vep_cache                    = null
+    run_vep                      = false
+    filter                       = false
 
     // References
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes/'
-    igenomes_ignore            = false
+    genome                       = null
+    igenomes_base                = 's3://ngi-igenomes/igenomes/'
+    igenomes_ignore              = false
 
     // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    multiqc_logo               = null
-    max_multiqc_email_size     = '25.MB'
-    multiqc_methods_description = null
+    multiqc_config               = null
+    multiqc_title                = null
+    multiqc_logo                 = null
+    max_multiqc_email_size       = '25.MB'
+    multiqc_methods_description  = null
 
     // Boilerplate options
     outdir                       = null
@@ -42,20 +42,19 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+    trace_report_suffix          = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
 
     // Config options
-    config_profile_name        = null
-    config_profile_description = null
+    config_profile_name          = null
+    config_profile_description   = null
 
-    custom_config_version      = 'master'
-    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    config_profile_contact     = null
-    config_profile_url         = null
+    custom_config_version        = 'master'
+    custom_config_base           = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    config_profile_contact       = null
+    config_profile_url           = null
 
     // Schema validation default options
-    validate_params            = true
-
+    validate_params              = true
 }
 
 // Load base.config by default for all pipelines
@@ -63,40 +62,40 @@ includeConfig 'conf/base.config'
 
 profiles {
     debug {
-        dumpHashes              = true
-        process.beforeScript    = 'echo $HOSTNAME'
-        cleanup                 = false
+        dumpHashes                                   = true
+        process.beforeScript                         = 'echo $HOSTNAME'
+        cleanup                                      = false
         nextflow.enable.configProcessNamesValidation = true
     }
     conda {
-        conda.enabled           = true
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda']
-        apptainer.enabled       = false
+        conda.enabled        = true
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
+        conda.channels       = ['conda-forge', 'bioconda']
+        apptainer.enabled    = false
     }
     mamba {
-        conda.enabled           = true
-        conda.useMamba          = true
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
+        conda.enabled        = true
+        conda.useMamba       = true
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
+        apptainer.enabled    = false
     }
     docker {
-        docker.enabled          = true
-        conda.enabled           = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
-        docker.runOptions       = '-u $(id -u):$(id -g)'
+        docker.enabled       = true
+        conda.enabled        = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
+        apptainer.enabled    = false
+        docker.runOptions    = '-u $(id -u):$(id -g)'
     }
     arm64 {
         process.arch            = 'arm64'
@@ -110,54 +109,54 @@ profiles {
         wave.strategy           = 'conda,container'
     }
     emulate_amd64 {
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
-        singularity.enabled     = true
-        singularity.autoMounts  = true
-        conda.enabled           = false
-        docker.enabled          = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
+        singularity.enabled    = true
+        singularity.autoMounts = true
+        conda.enabled          = false
+        docker.enabled         = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+        apptainer.enabled      = false
     }
     podman {
-        podman.enabled          = true
-        conda.enabled           = false
-        docker.enabled          = false
-        singularity.enabled     = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
+        podman.enabled       = true
+        conda.enabled        = false
+        docker.enabled       = false
+        singularity.enabled  = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
+        apptainer.enabled    = false
     }
     shifter {
-        shifter.enabled         = true
-        conda.enabled           = false
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        charliecloud.enabled    = false
-        apptainer.enabled       = false
+        shifter.enabled      = true
+        conda.enabled        = false
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        charliecloud.enabled = false
+        apptainer.enabled    = false
     }
     charliecloud {
-        charliecloud.enabled    = true
-        conda.enabled           = false
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        apptainer.enabled       = false
+        charliecloud.enabled = true
+        conda.enabled        = false
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        apptainer.enabled    = false
     }
     apptainer {
-        apptainer.enabled       = true
-        apptainer.autoMounts    = true
-        conda.enabled           = false
-        docker.enabled          = false
-        singularity.enabled     = false
-        podman.enabled          = false
-        shifter.enabled         = false
-        charliecloud.enabled    = false
+        apptainer.enabled    = true
+        apptainer.autoMounts = true
+        conda.enabled        = false
+        docker.enabled       = false
+        singularity.enabled  = false
+        podman.enabled       = false
+        shifter.enabled      = false
+        charliecloud.enabled = false
     }
     wave {
         apptainer.ociAutoPull   = true
@@ -167,20 +166,22 @@ profiles {
         wave.strategy           = 'conda,container'
     }
     gpu {
-        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
-        apptainer.runOptions    = '--nv'
-        singularity.runOptions  = '--nv'
+        docker.runOptions      = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions   = '--nv'
+        singularity.runOptions = '--nv'
+    }
+    test {
+        includeConfig 'conf/test.config'
     }
-    test { includeConfig 'conf/test.config' }
 }
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
-apptainer.registry    = 'quay.io'
-docker.registry       = 'quay.io'
-podman.registry       = 'quay.io'
-singularity.registry  = 'quay.io'
+apptainer.registry = 'quay.io'
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+singularity.registry = 'quay.io'
 charliecloud.registry = 'quay.io'
 
 // Load nf-core custom profiles from different institutions                                                                                                                 │
@@ -202,11 +203,11 @@ env {
 // Set bash options
 process.shell = [
     "bash",
-    "-C",         // No clobber - prevent output redirection from overwriting files.
-    "-e",         // Exit if a tool returns a non-zero status/exit code
-    "-u",         // Treat unset variables and parameters as an error
-    "-o",         // Returns the status of the last command to exit..
-    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+    "-C",
+    "-e",
+    "-u",
+    "-o",
+    "pipefail",
 ]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
@@ -238,7 +239,7 @@ manifest {
             email: '',
             github: '@SusiJo',
             contribution: ['author'],
-            orcid: '0009-0001-9152-7291'
+            orcid: '0009-0001-9152-7291',
         ],
         [
             name: 'Friederike Hanssen',
@@ -246,7 +247,7 @@ manifest {
             email: '',
             github: '@FriederikeHanssen',
             contribution: ['author'],
-            orcid: '0009-0001-9875-5262'
+            orcid: '0009-0001-9875-5262',
         ],
         [
             name: 'Famke Bäuerle',
@@ -254,8 +255,8 @@ manifest {
             email: 'famke.baeuerle@uni-tuebingen.de',
             github: '@famosab',
             contribution: ['maintainer'],
-            orcid: '0000-0003-1387-0251'
-        ]
+            orcid: '0000-0003-1387-0251',
+        ],
     ]
     homePage        = 'https://github.com/qbic-pipelines/vcftomaf'
     description     = """Convert vcf files to maf format"""
@@ -268,16 +269,16 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.5.1'
 }
 
 validation {
     defaultIgnoreParams = ["genomes"]
-    monochromeLogs = params.monochrome_logs
+    monochromeLogs      = params.monochrome_logs
     help {
-        enabled = true
-        command = "nextflow run qbic-pipelines/vcftomaf -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
-        fullParameter = "help_full"
+        enabled             = true
+        command             = "nextflow run qbic-pipelines/vcftomaf -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        fullParameter       = "help_full"
         showHiddenParameter = "show_hidden"
     }
 }
diff --git a/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf b/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf
index def884d..922bcad 100644
--- a/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_vcftomaf_pipeline/main.nf
@@ -8,15 +8,15 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap          } from 'plugin/nf-schema'
-include { samplesheetToList         } from 'plugin/nf-schema'
-include { paramsHelp                } from 'plugin/nf-schema'
-include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
-include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
-include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN   } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap        } from 'plugin/nf-schema'
+include { samplesheetToList       } from 'plugin/nf-schema'
+include { paramsHelp              } from 'plugin/nf-schema'
+include { completionEmail         } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary       } from '../../nf-core/utils_nfcore_pipeline'
+include { imNotification          } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE   } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -25,7 +25,6 @@ include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipelin
 */
 
 workflow PIPELINE_INITIALISATION {
-
     take:
     version           // boolean: Display version and exit
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
@@ -44,11 +43,11 @@ workflow PIPELINE_INITIALISATION {
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
-    UTILS_NEXTFLOW_PIPELINE (
+    UTILS_NEXTFLOW_PIPELINE(
         version,
         true,
         outdir,
-        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1
+        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1,
     )
 
     //
@@ -56,7 +55,7 @@ workflow PIPELINE_INITIALISATION {
     //
     command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
 
-    UTILS_NFSCHEMA_PLUGIN (
+    UTILS_NFSCHEMA_PLUGIN(
         workflow,
         validate_params,
         null,
@@ -65,13 +64,13 @@ workflow PIPELINE_INITIALISATION {
         show_hidden,
         "",
         "",
-        command
+        command,
     )
 
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE (
+    UTILS_NFCORE_PIPELINE(
         nextflow_cli_args
     )
 
@@ -83,22 +82,22 @@ workflow PIPELINE_INITIALISATION {
     //
     // Create channel from input file provided through params.input
     //
-    ch_samplesheet = Channel
-        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
-        .map{ meta, normal_id, tumor_id, vcf_normal_id, vcf_tumor_id, vcf, index ->
+    ch_samplesheet = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .map { meta, normal_id, tumor_id, vcf_normal_id, vcf_tumor_id, vcf, index ->
 
-            meta.index               = index     ? true      : false
+            meta.index = index ? true : false
 
             if (normal_id) {
-                meta.normal_id       = normal_id
-                meta.vcf_normal_id   = vcf_normal_id
+                meta.normal_id = normal_id
+                meta.vcf_normal_id = vcf_normal_id
             }
             if (tumor_id) {
-                meta.tumor_id        = tumor_id
-                meta.vcf_tumor_id    = vcf_tumor_id
+                meta.tumor_id = tumor_id
+                meta.vcf_tumor_id = vcf_tumor_id
             }
-            return [meta, vcf, index] // it[0], it[1], it[2]
+            return [meta, vcf, index]
         }
+
     emit:
     samplesheet = ch_samplesheet
     versions    = ch_versions
@@ -111,7 +110,6 @@ workflow PIPELINE_INITIALISATION {
 */
 
 workflow PIPELINE_COMPLETION {
-
     take:
     email           //  string: email address
     email_on_fail   //  string: email address sent on pipeline failure
@@ -148,7 +146,7 @@ workflow PIPELINE_COMPLETION {
     }
 
     workflow.onError {
-        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+        log.error("Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting")
     }
 }
 
@@ -171,20 +169,20 @@ def validateInputSamplesheet(input) {
     def (metas, fastqs) = input[1..2]
 
     // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end
-    def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1
+    def endedness_ok = metas.collect { meta -> meta.single_end }.unique().size == 1
     if (!endedness_ok) {
         error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}")
     }
 
-    return [ metas[0], fastqs ]
+    return [metas[0], fastqs]
 }
 //
 // Get attribute from genome config file e.g. fasta
 //
 def getGenomeAttribute(attribute) {
     if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey(attribute)) {
-            return params.genomes[ params.genome ][ attribute ]
+        if (params.genomes[params.genome].containsKey(attribute)) {
+            return params.genomes[params.genome][attribute]
         }
     }
     return null
@@ -195,11 +193,7 @@ def getGenomeAttribute(attribute) {
 //
 def genomeExistsError() {
     if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-            "  Currently, the available genome keys are:\n" +
-            "  ${params.genomes.keySet().join(", ")}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + "  Currently, the available genome keys are:\n" + "  ${params.genomes.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
         error(error_string)
     }
 }
@@ -211,10 +205,10 @@ def toolCitationText() {
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
-            "Tools used in the workflow included:",
-            "MultiQC (Ewels et al. 2016)",
-            "."
-        ].join(' ').trim()
+        "Tools used in the workflow included:",
+        "MultiQC (Ewels et al. 2016)",
+        ".",
+    ].join(' ').trim()
 
     return citation_text
 }
@@ -224,8 +218,8 @@ def toolBibliographyText() {
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
-        ].join(' ').trim()
+        "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+    ].join(' ').trim()
 
     return reference_text
 }
@@ -247,7 +241,10 @@ def methodsDescriptionText(mqc_methods_yaml) {
             temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
         }
         meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
-    } else meta["doi_text"] = ""
+    }
+    else {
+        meta["doi_text"] = ""
+    }
     meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
@@ -261,7 +258,7 @@ def methodsDescriptionText(mqc_methods_yaml) {
 
     def methods_text = mqc_methods_yaml.text
 
-    def engine =  new groovy.text.SimpleTemplateEngine()
+    def engine = new groovy.text.SimpleTemplateEngine()
     def description_html = engine.createTemplate(methods_text).make(meta)
 
     return description_html.toString()
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 1ce02bc..56b8d6a 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -4,13 +4,13 @@
             8,
             {
                 "BCFTOOLS_VIEW": {
-                    "bcftools": 1.2
+                    "bcftools": 1.22
                 },
                 "GUNZIP": {
-                    "gunzip": 1.1
+                    "gunzip": 1.13
                 },
                 "TABIX_TABIX": {
-                    "tabix": 1.2
+                    "tabix": 1.21
                 },
                 "VCF2MAF": {
                     "vcf2maf": "1.6.22"
@@ -51,8 +51,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-05-06T14:41:18.473188"
+        "timestamp": "2025-12-10T13:25:39.05212212"
     }
 }
\ No newline at end of file
diff --git a/tests/vep.nf.test.snap b/tests/vep.nf.test.snap
index 3fcee3d..fd280ab 100644
--- a/tests/vep.nf.test.snap
+++ b/tests/vep.nf.test.snap
@@ -4,13 +4,13 @@
             9,
             {
                 "BCFTOOLS_VIEW": {
-                    "bcftools": 1.2
+                    "bcftools": 1.22
                 },
                 "GUNZIP": {
-                    "gunzip": 1.1
+                    "gunzip": 1.13
                 },
                 "TABIX_TABIX": {
-                    "tabix": 1.2
+                    "tabix": 1.21
                 },
                 "UNTAR": {
                     "untar": 1.34
@@ -55,8 +55,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-05-06T14:40:45.144536"
+        "timestamp": "2025-12-10T13:28:44.643003247"
     }
 }
\ No newline at end of file
diff --git a/workflows/vcftomaf/main.nf b/workflows/vcftomaf/main.nf
index f5536a9..8a1c65b 100644
--- a/workflows/vcftomaf/main.nf
+++ b/workflows/vcftomaf/main.nf
@@ -7,17 +7,17 @@
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { BCFTOOLS_VIEW               } from '../../modules/nf-core/bcftools/view/main'
-include { GUNZIP                      } from '../../modules/nf-core/gunzip/main'
-include { MULTIQC                     } from '../../modules/nf-core/multiqc/main'
-include { PICARD_LIFTOVERVCF          } from '../../modules/nf-core/picard/liftovervcf/main'
-include { TABIX_TABIX                 } from '../../modules/nf-core/tabix/tabix/main'
-include { UNTAR                       } from '../../modules/nf-core/untar/main'
-include { VCF2MAF                     } from '../../modules/nf-core/vcf2maf/main'
-include { paramsSummaryMap            } from 'plugin/nf-schema'
-include { paramsSummaryMultiqc        } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
-include { softwareVersionsToYAML      } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText      } from '../../subworkflows/local/utils_nfcore_vcftomaf_pipeline'
+include { BCFTOOLS_VIEW          } from '../../modules/nf-core/bcftools/view/main'
+include { GUNZIP                 } from '../../modules/nf-core/gunzip/main'
+include { MULTIQC                } from '../../modules/nf-core/multiqc/main'
+include { PICARD_LIFTOVERVCF     } from '../../modules/nf-core/picard/liftovervcf/main'
+include { TABIX_TABIX            } from '../../modules/nf-core/tabix/tabix/main'
+include { UNTAR                  } from '../../modules/nf-core/untar/main'
+include { VCF2MAF                } from '../../modules/nf-core/vcf2maf/main'
+include { paramsSummaryMap       } from 'plugin/nf-schema'
+include { paramsSummaryMultiqc   } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline'
+include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_vcftomaf_pipeline'
 
 
 /*
@@ -27,19 +27,16 @@ include { methodsDescriptionText      } from '../../subworkflows/local/utils_nfc
 */
 
 workflow VCFTOMAF {
-
     take:
-    ch_samplesheet // channel: samplesheet read in from --input
+    ch_samplesheet     // channel: samplesheet read in from --input
     intervals
     fasta
     dict
     liftover_chain
-    genome
     vep_cache
     vep_cache_unpacked
 
     main:
-
     ch_versions = channel.empty()
     ch_multiqc_files = channel.empty()
 
@@ -47,34 +44,29 @@ workflow VCFTOMAF {
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files
     //
 
-    if (params.vep_cache){
-        ch_vep_cache = vep_cache.map{
-            it -> def new_id = ""
-                if(it) {
-                    new_id = it[0].simpleName.toString()
-                }
-            [[id:new_id], it]
-        }
+    if (params.vep_cache) {
+        ch_vep_cache = vep_cache.map { it -> [[id: it[0].simpleName.toString()], it] }
         // UNTAR if available
-        vep_cache_unpacked  = UNTAR(ch_vep_cache).untar.map { it[1] }
-        ch_versions         = ch_versions.mix(UNTAR.out.versions)
+        vep_cache_unpacked = UNTAR(ch_vep_cache).untar.map { unpacked -> unpacked[1] }
+        ch_versions = ch_versions.mix(UNTAR.out.versions)
     }
 
     // BRANCH CHANNEL
-    ch_samplesheet.branch{
-        is_indexed:  it[0].index == true
-        to_index:    it[0].index == false
-    }.set{ch_input}
+    ch_samplesheet
+        .branch { it ->
+            is_indexed: it[0].index == true
+            to_index: it[0].index == false
+        }
+        .set { ch_input }
 
     // Remove empty index [] from channel = it[2]
-    input_to_index = ch_input.to_index.map{ it -> [it[0], it[1]] }
+    input_to_index = ch_input.to_index.map { it -> [it[0], it[1]] }
 
     // Create tbi index only if not provided
     TABIX_TABIX(input_to_index)
-    ch_versions = ch_versions.mix(TABIX_TABIX.out.versions.first())
 
     // Join tbi index back to input
-    ch_indexed_to_index = input_to_index.join(TABIX_TABIX.out.tbi)
+    ch_indexed_to_index = input_to_index.join(TABIX_TABIX.out.index)
 
     // Join both channels back together
     ch_vcf = ch_input.is_indexed.mix(ch_indexed_to_index)
@@ -82,23 +74,25 @@ workflow VCFTOMAF {
     //
     // MODULE: Run PASS + BED filtering
     //
-    BCFTOOLS_VIEW (
+    BCFTOOLS_VIEW(
         ch_vcf,
         intervals,
-        [],  // targets
-        []   // samples
+        [],
+        [],
     )
 
     ch_versions = ch_versions.mix(BCFTOOLS_VIEW.out.versions.first())
 
     ch_gunzip = BCFTOOLS_VIEW.out.vcf
 
-    if(params.liftover_chain){
+    if (params.liftover_chain) {
 
-        PICARD_LIFTOVERVCF(BCFTOOLS_VIEW.out.vcf,
-                            dict.map{ it -> [ [ id:it.baseName ], it ] },
-                            fasta.map{ it -> [ [ id:it.baseName ], it ] },
-                            liftover_chain.map{ it -> [ [ id:it.baseName ], it ] })
+        PICARD_LIFTOVERVCF(
+            BCFTOOLS_VIEW.out.vcf,
+            dict.map { it -> [[id: it.baseName], it] },
+            fasta.map { it -> [[id: it.baseName], it] },
+            liftover_chain.map { it -> [[id: it.baseName], it] },
+        )
         ch_gunzip = PICARD_LIFTOVERVCF.out.vcf_lifted
         ch_versions = ch_versions.mix(PICARD_LIFTOVERVCF.out.versions.first())
     }
@@ -113,7 +107,7 @@ workflow VCFTOMAF {
     VCF2MAF(
         GUNZIP.out.gunzip,
         fasta,
-        vep_cache_unpacked
+        vep_cache_unpacked,
     )
 
     ch_versions = ch_versions.mix(VCF2MAF.out.versions.first())
@@ -121,7 +115,8 @@ workflow VCFTOMAF {
     //
     // Collate and save software versions
     //
-    def topic_versions = channel.topic("versions")
+    def topic_versions = channel
+        .topic("versions")
         .distinct()
         .branch { entry ->
             versions_file: entry instanceof Path
@@ -151,33 +146,27 @@ workflow VCFTOMAF {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config                     = channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config              = params.multiqc_config ? channel.fromPath(params.multiqc_config, checkIfExists: true) : channel.empty()
-    ch_multiqc_logo                       = params.multiqc_logo ? channel.fromPath(params.multiqc_logo, checkIfExists: true) : channel.empty()
-    summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary                   = channel.value(paramsSummaryMultiqc(summary_params))
-    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
-    ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
-
-    MULTIQC (
+    ch_multiqc_config = channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config = params.multiqc_config ? channel.fromPath(params.multiqc_config, checkIfExists: true) : channel.empty()
+    ch_multiqc_logo = params.multiqc_logo ? channel.fromPath(params.multiqc_logo, checkIfExists: true) : channel.empty()
+    summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
+    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
+    ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("${projectDir}/assets/methods_description_template.yml", checkIfExists: true)
+    ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+    ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)
+    ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))
+
+    MULTIQC(
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),
         ch_multiqc_custom_config.toList(),
         ch_multiqc_logo.toList(),
         [],
-        []
+        [],
     )
 
     emit:
     multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html
-    versions       = ch_versions                 // channel: [ path(versions.yml) ]
+    versions       = ch_versions // channel: [ path(versions.yml) ]
 }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/