diff --git a/.nf-core.yml b/.nf-core.yml
index 0f557db5..061ecb02 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1,29 +1,29 @@
 repository_type: pipeline
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-sash_logo_light.png
-  - docs/images/nf-core-sash_logo_light.png
-  - docs/images/nf-core-sash_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
-  - .github/ISSUE_TEMPLATE/bug_report.yml
-  - .github/workflows/branch.yml
-  - .github/workflows/ci.yml
-  - .github/workflows/linting_comment.yml
-  - .github/workflows/linting.yml
-  - conf/igenomes.config
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-sash_logo_light.png
+    - docs/images/nf-core-sash_logo_light.png
+    - docs/images/nf-core-sash_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/ci.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - conf/igenomes.config
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
-  - process.cpus
-  - process.memory
-  - process.time
-  - custom_config
+    - manifest.name
+    - manifest.homePage
+    - process.cpus
+    - process.memory
+    - process.time
+    - custom_config
   multiqc_config:
-  - report_comment
+    - report_comment
   files_unchanged:
-  - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/bug_report.yml
   readme:
-  - nextflow_badge
+    - nextflow_badge
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 21dc74a4..7f47fe17 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -113,9 +113,9 @@ Initial release of umccr/sash, created with the [nf-core](https://nf-co.re/) tem
 
 ### Dependencies
 
-| Tool | Old | New |
-|------|-----|-----|
-| Linx | 1.25 | 2.0 |
-| Purple | 4.0.1 | 4.1.0 |
-| Bolt | — | umccr/bolt#6 |
-| GPGR | — | umccr/gpgr#88 |
+| Tool   | Old   | New           |
+| ------ | ----- | ------------- |
+| Linx   | 1.25  | 2.0           |
+| Purple | 4.0.1 | 4.1.0         |
+| Bolt   | —     | umccr/bolt#6  |
+| GPGR   | —     | umccr/gpgr#88 |
diff --git a/README.md b/README.md
index 6c534c11..bee0ac9b 100644
--- a/README.md
+++ b/README.md
@@ -11,9 +11,9 @@ functionality.
 
 ## Table of contents
 
-* [Summary](#summary)
-* [Requirements](#requirements)
-* [Usage](#usage)
+- [Summary](#summary)
+- [Requirements](#requirements)
+- [Usage](#usage)
 
 ## Summary
 
diff --git a/conf/modules.config b/conf/modules.config
index 0dc483aa..730e5af5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -57,7 +57,7 @@ process {
 
                 if (fp.equals('versions.yml')) {
                     return null
-                } else if (fp.matches('output/.*.pcgr_acmg.grch38.html')) {
+                } else if (fp.matches('output/.*.pcgr.grch38.html')) {
                     return "${meta.key}/${meta.tumor_id}.pcgr.html"
                 } else {
                     def fp_out = fp.replaceFirst(/output\//, '')
@@ -126,7 +126,30 @@ process {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/${filename}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/${filename}" }
+        ]
+    }
+
+
+    withName: 'SIGRAP_HRDETECT' {
+        publishDir = [
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/sigrap/hrdetect/${filename}" }
+        ]
+    }
+
+    withName: 'SIGRAP_MUTPAT' {
+        publishDir = [
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> 
+                if (filename.equals('versions.yml')) {
+                    return null
+                } else {
+                    return "${meta.key}/sigrap/${filename}"
+                }
+            }
         ]
     }
 
@@ -212,4 +235,12 @@ process {
         ]
     }
 
+    withName: 'VCF2MAF' {
+        publishDir = [
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/vcf2maf/${filename}" },
+        ]
+    }
+
 }
diff --git a/conf/refdata.config b/conf/refdata.config
index 6bef3738..f57e5cf2 100644
--- a/conf/refdata.config
+++ b/conf/refdata.config
@@ -4,7 +4,7 @@ params {
         umccr_reference_data = '2--0'
         hmf_reference_data = 'hmf_pipeline_resources.38_v2.2.0--3'
 
-        pcgr = '20220203'
+        pcgr = '20250314'
         snpeff = '5_1'
 
         oncokb = '4.12'
@@ -20,7 +20,8 @@ params {
     }
 
     miscdata_paths {
-        pcgr_dir = "databases/pcgr/v${params.data_versions.pcgr}/"
+        pcgr_dir = "databases/pcgr/pcgr_ref_data.${params.data_versions.pcgr}.grch38.tgz"
+        vep_dir = "databases/pcgr/homo_sapiens_vep_113_GRCh38.tar.gz"
         snpeff_dir = "databases/snpeff/v${params.data_versions.snpeff}/"
 
         oncokb_genes = "databases/oncokb/v${params.data_versions.oncokb}/cancerGeneList.txt"
diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index 19469ca1..dff58fae 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,10 +2,10 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17-gpgr'
+    container 'docker.io/qclayssen/bolt:0.3.0-dev-14-gpgr'
 
     input:
-    tuple val(meta), path(smlv_somatic_vcf), path(smlv_somatic_bcftools_stats), path(smlv_somatic_counts_process), path(sv_somatic_tsv), path(sv_somatic_vcf), path(cnv_somatic_tsv), path(af_global), path(af_keygenes), path(purple_baf_plot), path(purple_dir), path(virusbreakend_dir), path(dragen_hrd)
+    tuple val(meta), path(smlv_somatic_vcf), path(smlv_somatic_bcftools_stats), path(smlv_somatic_counts_process), path(sv_somatic_tsv), path(sv_somatic_vcf), path(cnv_somatic_tsv), path(af_global), path(af_keygenes), path(purple_baf_plot), path(purple_dir), path(virusbreakend_dir), path(dragen_hrd), path(smlv_somatic_mutpat), path(smlv_somatic_hrdetect), path(smlv_somatic_chord)
     path somatic_driver_panel
     path oncokb_genes
 
@@ -35,6 +35,10 @@ process BOLT_OTHER_CANCER_REPORT {
         --smlv_somatic_bcftools_stats_fp \$(pwd)/${smlv_somatic_bcftools_stats} \\
         --smlv_somatic_counts_process_fp \$(pwd)/${smlv_somatic_counts_process} \\
         \\
+        --mutpat_dir \$(pwd)/${smlv_somatic_mutpat} \\
+        --hrdetect_file \$(pwd)/${smlv_somatic_hrdetect} \\
+        --chord_file \$(pwd)/${smlv_somatic_chord} \\
+        \\
         --sv_somatic_tsv_fp \$(pwd)/${sv_somatic_tsv} \\
         --sv_somatic_vcf_fp \$(pwd)/${sv_somatic_vcf} \\
         --cnv_somatic_tsv_fp \$(pwd)/${cnv_somatic_tsv} \\
diff --git a/modules/local/bolt/other/multiqc_report/main.nf b/modules/local/bolt/other/multiqc_report/main.nf
index f26d6921..a5752f09 100644
--- a/modules/local/bolt/other/multiqc_report/main.nf
+++ b/modules/local/bolt/other/multiqc_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_MULTIQC_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17-multiqc'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20-multiqc'
 
     input:
     tuple val(meta), path(input_files)
diff --git a/modules/local/bolt/other/purple_baf_plot/main.nf b/modules/local/bolt/other/purple_baf_plot/main.nf
index c52d8202..6ccb318a 100644
--- a/modules/local/bolt/other/purple_baf_plot/main.nf
+++ b/modules/local/bolt/other/purple_baf_plot/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_PURPLE_BAF_PLOT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17-circos'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20-circos'
 
     input:
     tuple val(meta), path(purple_dir)
diff --git a/modules/local/bolt/smlv_germline/prepare/main.nf b/modules/local/bolt/smlv_germline/prepare/main.nf
index 2fc3cc4a..615078dd 100644
--- a/modules/local/bolt/smlv_germline/prepare/main.nf
+++ b/modules/local/bolt/smlv_germline/prepare/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_GERMLINE_PREPARE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20'
 
     input:
     tuple val(meta), path(smlv_vcf)
diff --git a/modules/local/bolt/smlv_germline/report/main.nf b/modules/local/bolt/smlv_germline/report/main.nf
index 3f5fdea9..0acfffde 100644
--- a/modules/local/bolt/smlv_germline/report/main.nf
+++ b/modules/local/bolt/smlv_germline/report/main.nf
@@ -2,12 +2,13 @@ process BOLT_SMLV_GERMLINE_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_unfiltered_vcf)
     path germline_predisposition_panel_genes
     path pcgr_data_dir
+    path vep_dir
 
     output:
     tuple val(meta), path("output/*.variant_counts_type.yaml"), emit: counts_type
@@ -32,6 +33,7 @@ process BOLT_SMLV_GERMLINE_REPORT {
         --pcgrr_conda pcgrr \\
         --germline_panel_list_fp ${germline_predisposition_panel_genes} \\
         --pcgr_data_dir ${pcgr_data_dir} \\
+        --vep_dir ${vep_dir} \\
         --threads ${task.cpus} \\
         --output_dir output/
 
diff --git a/modules/local/bolt/smlv_somatic/annotate/main.nf b/modules/local/bolt/smlv_somatic/annotate/main.nf
index d28aeeb4..f6bb82cc 100644
--- a/modules/local/bolt/smlv_somatic/annotate/main.nf
+++ b/modules/local/bolt/smlv_somatic/annotate/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_ANNOTATE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf)
@@ -10,6 +10,7 @@ process BOLT_SMLV_SOMATIC_ANNOTATE {
     path annotations_dir
     path pon_dir
     path pcgr_data_dir
+    path vep_dir
 
     output:
     tuple val(meta), path("output/${meta.tumor_id}.annotations.vcf.gz"), emit: vcf
@@ -19,7 +20,7 @@ process BOLT_SMLV_SOMATIC_ANNOTATE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def chunk_size_arg = params.pcgr_variant_chunk_size ? "--pcgr_variant_chunk_size ${params.pcgr_variant_chunk_size}" : ''
 
     """
     bolt smlv_somatic annotate \\
@@ -30,10 +31,12 @@ process BOLT_SMLV_SOMATIC_ANNOTATE {
         --annotations_dir ${annotations_dir} \\
         --pon_dir ${pon_dir} \\
         --pcgr_data_dir ${pcgr_data_dir} \\
+        --vep_dir ${vep_dir} \\
         --pcgr_conda pcgr \\
         --pcgrr_conda pcgrr \\
         --threads ${task.cpus} \\
-        --output_dir output/
+        --output_dir output/ \\
+        ${chunk_size_arg}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/bolt/smlv_somatic/filter/main.nf b/modules/local/bolt/smlv_somatic/filter/main.nf
index 93519a82..f76db5f8 100644
--- a/modules/local/bolt/smlv_somatic/filter/main.nf
+++ b/modules/local/bolt/smlv_somatic/filter/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_FILTER {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20'
 
     input:
     tuple val(meta), path(smlv_vcf)
diff --git a/modules/local/bolt/smlv_somatic/report/main.nf b/modules/local/bolt/smlv_somatic/report/main.nf
index cbc160c1..15225680 100644
--- a/modules/local/bolt/smlv_somatic/report/main.nf
+++ b/modules/local/bolt/smlv_somatic/report/main.nf
@@ -2,11 +2,12 @@ process BOLT_SMLV_SOMATIC_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_filters_vcf), path(smlv_dragen_vcf), path(purple_purity)
     path pcgr_data_dir
+    path vep_dir
     path somatic_driver_panel_regions_coding
     path giab_regions
     path genome_fasta
@@ -19,7 +20,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
     tuple val(meta), path("output/*.variant_counts_type.yaml")   , emit: counts_type
     tuple val(meta), path("output/*.variant_counts_process.json"), emit: counts_process
     path 'output/pcgr/'                                          , emit: pcgr_dir
-    path "output/*.pcgr_acmg.grch38.html"                        , emit: pcgr_report
+    path "output/*.pcgr.grch38.html"                        , emit: pcgr_report
     path 'versions.yml'                                          , emit: versions
 
     when:
@@ -40,6 +41,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
         --pcgr_conda pcgr \\
         --pcgrr_conda pcgrr \\
         --pcgr_data_dir ${pcgr_data_dir} \\
+        --vep_dir ${vep_dir} \\
         --purple_purity_fp ${purple_purity} \\
         \\
         --cancer_genes_fp ${somatic_driver_panel_regions_coding} \\
@@ -49,7 +51,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
         --threads ${task.cpus} \\
         --output_dir output/
 
-    mv output/pcgr/${meta.tumor_id}.pcgr_acmg.grch38.html output/
+    mv output/pcgr/${meta.tumor_id}.pcgr.grch38.html output/
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -66,7 +68,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
     touch output/${meta.tumor_id}.somatic.variant_counts_type.yaml
     touch output/${meta.tumor_id}.somatic.variant_counts_process.json
     touch output/${meta.tumor_id}.somatic.bcftools_stats.txt
-    touch output/${meta.tumor_id}.pcgr_acmg.grch38.html
+    touch output/${meta.tumor_id}.pcgr.grch38.html
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/bolt/smlv_somatic/rescue/main.nf b/modules/local/bolt/smlv_somatic/rescue/main.nf
index 2e1ac64b..f274231d 100644
--- a/modules/local/bolt/smlv_somatic/rescue/main.nf
+++ b/modules/local/bolt/smlv_somatic/rescue/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_RESCUE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_tbi), path(sage_smlv_vcf), path(sage_smlv_tbi)
diff --git a/modules/local/bolt/sv_somatic/annotate/main.nf b/modules/local/bolt/sv_somatic/annotate/main.nf
index af48b4f5..ecd27b5c 100644
--- a/modules/local/bolt/sv_somatic/annotate/main.nf
+++ b/modules/local/bolt/sv_somatic/annotate/main.nf
@@ -2,7 +2,7 @@ process BOLT_SV_SOMATIC_ANNOTATE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17-snpeff'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20-snpeff'
 
     input:
     tuple val(meta), path(sv_vcf), path(cnv_tsv)
diff --git a/modules/local/bolt/sv_somatic/prioritise/main.nf b/modules/local/bolt/sv_somatic/prioritise/main.nf
index 710cb192..4f78b51b 100644
--- a/modules/local/bolt/sv_somatic/prioritise/main.nf
+++ b/modules/local/bolt/sv_somatic/prioritise/main.nf
@@ -2,7 +2,7 @@ process BOLT_SV_SOMATIC_PRIORITISE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17'
+    container 'ghcr.io/umccr/bolt:0.3.0-dev-20'
 
     input:
     tuple val(meta), path(sv_vcf)
diff --git a/modules/local/custom/extract_tarball/main.nf b/modules/local/custom/extract_tarball/main.nf
new file mode 100644
index 00000000..1ebc1011
--- /dev/null
+++ b/modules/local/custom/extract_tarball/main.nf
@@ -0,0 +1,33 @@
+process CUSTOM_EXTRACTTARBALL {
+    label 'process_single'
+
+    conda "conda-forge::tar=1.34"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'quay.io/nf-core/ubuntu:20.04' }"
+
+    input:
+    tuple val(meta), path(tarball)
+
+    output:
+    path "${meta.id}/", emit: extracted_dir
+    path '.command.*', emit: command_files
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def strip = meta.strip_components != null ? meta.strip_components : 1
+    def target = meta.subdir ? "${meta.id}/${meta.subdir}" : "${meta.id}"
+
+    """
+    mkdir -p ${target}
+    tar ${args} -xzvf ${tarball} --strip-components ${strip} -C ${target}/
+    """
+
+    stub:
+    """
+    mkdir -p ${meta.id}/
+    """
+}
diff --git a/modules/local/pave/somatic/meta.yml b/modules/local/pave/somatic/meta.yml
index 97aa6729..552537c4 100644
--- a/modules/local/pave/somatic/meta.yml
+++ b/modules/local/pave/somatic/meta.yml
@@ -12,7 +12,7 @@ tools:
       description: Annotates small variant VCF with gene, transcript coding and protein effects.
       homepage: https://github.com/hartwigmedical/hmftools/tree/master/pave
       documentation: https://github.com/hartwigmedical/hmftools/tree/master/pave
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
diff --git a/modules/local/sigrap/chord/main.nf b/modules/local/sigrap/chord/main.nf
new file mode 100644
index 00000000..44810f60
--- /dev/null
+++ b/modules/local/sigrap/chord/main.nf
@@ -0,0 +1,37 @@
+process SIGRAP_CHORD {
+    tag "${meta.id}"
+    label 'process_low'
+
+    container 'docker.io/qclayssen/sigrap:0.2.0-dev-7'
+
+    input:
+    tuple val(meta), path(chord_prediction_tsv)
+
+    output:
+    tuple val(meta), path('chord.json.gz')                  , emit: chord_json
+    path 'versions.yml'                                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    sigrap.R chord \\
+        --sample ${meta.id} \\
+        --chord ${chord_prediction_tsv} \\
+        --out chord.json.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sigrap: \$(sigrap.R --version | sed 's/^.*version //')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch chord.json.gz
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
+    """
+}
diff --git a/modules/local/sigrap/hrdetect/main.nf b/modules/local/sigrap/hrdetect/main.nf
new file mode 100644
index 00000000..8cb5fa57
--- /dev/null
+++ b/modules/local/sigrap/hrdetect/main.nf
@@ -0,0 +1,39 @@
+process SIGRAP_HRDETECT {
+    tag "${meta.id}"
+    label 'process_low'
+
+    container 'docker.io/qclayssen/sigrap:0.2.0-dev-7'
+
+    input:
+    tuple val(meta), path(smlv_somatic_vcf), path(sv_somatic_vcf), path(cnv_somatic_tsv)
+
+    output:
+    tuple val(meta), path('hrdetect.json.gz')                 , emit: hrdetect_json
+    path 'versions.yml'                                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    sigrap.R hrdetect \\
+        --sample ${meta.id} \\
+        --snv ${smlv_somatic_vcf} \\
+        --sv ${sv_somatic_vcf} \\
+        --cnv ${cnv_somatic_tsv} \\
+        --out  hrdetect.json.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sigrap: \$(sigrap.R --version | sed 's/^.*version //')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch hrdetect.json.gz
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
+    """
+}
diff --git a/modules/local/sigrap/mutpat/main.nf b/modules/local/sigrap/mutpat/main.nf
new file mode 100644
index 00000000..b4b34102
--- /dev/null
+++ b/modules/local/sigrap/mutpat/main.nf
@@ -0,0 +1,41 @@
+process SIGRAP_MUTPAT {
+    tag "${meta.id}"
+    label 'process_low'
+
+    container 'docker.io/qclayssen/sigrap:0.2.0-dev-7'
+
+    input:
+    tuple val(meta), path(smlv_somatic_vcf)
+
+    output:
+    tuple val(meta), path('mutpat/')                   , emit: mutpat_output
+    path 'versions.yml'                                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    sigrap.R mutpat \\
+        --sample ${meta.id} \\
+        --snv ${smlv_somatic_vcf} \\
+        --rainfall \\
+        --strand-bias \\
+        --predefined-dbs-mbs \\
+        --out mutpat/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sigrap: \$(sigrap.R --version | sed 's/^.*version //')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir -p sigrap/mutpat/
+    touch sigrap/mutpat/stub_output
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
+    """
+}
diff --git a/modules/local/vcf2maf/main.nf b/modules/local/vcf2maf/main.nf
new file mode 100644
index 00000000..707f7510
--- /dev/null
+++ b/modules/local/vcf2maf/main.nf
@@ -0,0 +1,50 @@
+process VCF2MAF {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    container 'quay.io/biocontainers/vcf2maf:1.6.22--hdfd78af_0'
+
+    input:
+    tuple val(meta), path(vcf)
+    path genome_fasta
+
+
+    output:
+    tuple val(meta), path("*.maf"), emit: maf
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    gunzip -c ${vcf} > ${meta.id}-temp.vcf
+
+    vcf2maf.pl \\
+        --inhibit-vep \\
+        --input-vcf ${meta.id}-temp.vcf \\
+        --output-maf ${meta.id}.maf \\
+        --ref-fasta ${genome_fasta} \\
+        --tumor-id ${meta.tumor_id} \\
+        --normal-id ${meta.normal_id} \\
+        --ncbi-build "GRCh38" \\
+        ${args}
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcf2maf: \$(vcf2maf.pl --help | grep -o 'vcf2maf [0-9.]*' | sed 's/vcf2maf //' || echo "1.6.22")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.maf
+
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
+    END_VERSIONS
+    """
+}
diff --git a/nextflow.config b/nextflow.config
index 00fc8aaf..479336a7 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -25,6 +25,7 @@ params {
     validate_params            = true
     show_hidden_params         = false
     schema_ignore_params       = 'hmfdata_paths,umccrdata_paths,miscdata_paths,data_versions,genome'
+    pcgr_variant_chunk_size    = null
 
     // Max resource options
     // Defaults only, expecting to be overwritten
@@ -143,6 +144,7 @@ env {
     R_PROFILE_USER   = "/.Rprofile"
     R_ENVIRON_USER   = "/.Renviron"
     JULIA_DEPOT_PATH = "/usr/local/share/julia"
+    XDG_CACHE_HOME   = "/tmp/quarto_cache_home"
 }
 
 // Capture exit codes from upstream processes when piping
@@ -174,7 +176,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.6'
     version         = '0.6.3'
-    doi             = ''
+    doi             = 'https://doi.org/10.5281/zenodo.15833493'
 }
 
 // Load modules.config for DSL2 module specific options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 47c839df..3d34050c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,10 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "input",
-                "outdir"
-            ],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -122,14 +119,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -179,6 +169,12 @@
                     "description": "Show all params when using `--help`",
                     "hidden": true,
                     "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
+                },
+                "pcgr_variant_chunk_size": {
+                    "type": "integer",
+                    "description": "Override maximum variants per PCGR chunk for the BOLT somatic annotate step.",
+                    "help_text": "Leave unset to use the default chunk size defined by BOLT. Provide an integer to adjust PCGR chunking behaviour when needed.",
+                    "fa_icon": "fas fa-database"
                 }
             }
         }
diff --git a/pipeline_template.yml b/pipeline_template.yml
index c8064235..9e816eb2 100644
--- a/pipeline_template.yml
+++ b/pipeline_template.yml
@@ -1,7 +1,7 @@
 prefix: umccr
 skip:
-- github
-- ci
-- github_badges
-- igenomes
-- nf_core_configs
+  - github
+  - ci
+  - github_badges
+  - igenomes
+  - nf_core_configs
diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 244ed699..ac3993c2 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -124,6 +124,13 @@ workflow PREPARE_INPUT {
             return [meta, virusbreakend_dir]
         }
 
+        // CHORD: homologous recombination deficiency prediction
+        // channel: [ meta, chord_prediction_tsv ]
+        ch_chord = ch_metas.map { meta ->
+            def base = file(meta.oncoanalyser_dir).toUriString()
+            return [meta, "${base}/chord/${meta.tumor_id}.chord.prediction.tsv"]
+        }
+
         // HRD: homologous recombination deficiency scores
         // channel: [ meta, hrdscore_csv ]
         ch_input_hrd = ch_metas.map { meta ->
@@ -173,6 +180,7 @@ workflow PREPARE_INPUT {
         cobalt           = ch_cobalt                  // channel: [ meta, cobalt_dir ]
         sage_somatic     = ch_sage_somatic            // channel: [ meta, sage_somatic_vcf, sage_somatic_tbi ]
         virusbreakend    = ch_virusbreakend           // channel: [ meta, virusbreakend_dir ]
+        chord            = ch_chord                   // channel: [ meta, chord_prediction_tsv ]
         call_inputs      = ch_call_inputs             // channel: [ meta_esvee, esvee_ref_depth_vcf, esvee_prep_dir ]
 
         // DRAGEN channels
diff --git a/subworkflows/local/prepare_reference.nf b/subworkflows/local/prepare_reference.nf
index 7ef91a5a..26115d7d 100644
--- a/subworkflows/local/prepare_reference.nf
+++ b/subworkflows/local/prepare_reference.nf
@@ -2,6 +2,8 @@
 // Prepare reference data as required
 //
 
+include { CUSTOM_EXTRACTTARBALL as DECOMP_MISC_DATA } from '../../modules/local/custom/extract_tarball/main'
+
 workflow PREPARE_REFERENCE {
     take:
 
@@ -18,6 +20,29 @@ workflow PREPARE_REFERENCE {
         ch_umccr_data = createDataMap(params.umccrdata_paths, umccr_reference_data_path)
         ch_misc_data = createDataMap(params.miscdata_paths, params.ref_data_path)
 
+        //
+        // Extract tarball resources (e.g. PCGR data, VEP cache) when provided as .tar.gz/.tgz
+        //
+        misc_tarball_inputs = getTarballInputs(params.miscdata_paths, params.ref_data_path)
+        if (misc_tarball_inputs) {
+            ch_misc_data_inputs = Channel.fromList(misc_tarball_inputs)
+            
+            DECOMP_MISC_DATA(ch_misc_data_inputs)
+
+            ch_misc_data_extracted = DECOMP_MISC_DATA.out.extracted_dir
+                .collect()
+                .map { dir_list ->
+                    // Convert list of directories to a map of [name: dir]
+                    def extracted_map = dir_list.collectEntries { dir ->
+                        [(dir.getFileName().toString()): dir]
+                    }
+                    // Merge extracted data with existing misc_data map
+                    return createDataMap(params.miscdata_paths, params.ref_data_path) + extracted_map
+                }
+            
+            ch_misc_data = ch_misc_data_extracted
+        }
+
         //
         // Prepare genome paths and info
         //
@@ -45,6 +70,34 @@ def createDataMap(entries, ref_data_base_path) {
         }
 }
 
+def getTarballInputs(entries, ref_data_base_path) {
+    return entries
+        .findAll { name, relpath ->
+            if (!relpath) {
+                return false
+            }
+            def rel = relpath.toString()
+            return rel.endsWith('.tar.gz') || rel.endsWith('.tgz')
+        }
+        .collect { name, relpath ->
+            def tarball = joinPath(ref_data_base_path, relpath)
+            def meta
+            if (name == 'vep_dir') {
+                // VEP cache: strip wrapper dir, extract into homo_sapiens subdir
+                // Result: vep_dir/homo_sapiens/113_GRCh38/
+                meta = [id: name, strip_components: 1, subdir: 'homo_sapiens']
+            } else if (name == 'pcgr_dir') {
+                // PCGR bundle: don't strip, tarball contains data/ directory
+                // Result: pcgr_dir/data/grch38/
+                meta = [id: name, strip_components: 0]
+            } else {
+                // Default: strip top-level wrapper directory
+                meta = [id: name, strip_components: 1]
+            }
+            return [meta, tarball]
+        }
+}
+
 def joinPath(a, b) {
     def a_noslash = file(a).toUriString().replaceAll('/$', '')
     return file("${a_noslash}/${b}", checkIfExists: true)
diff --git a/workflows/sash.nf b/workflows/sash.nf
index eb1bbb72..bad9c60d 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -42,13 +42,17 @@ include { BOLT_SMLV_GERMLINE_PREPARE } from '../modules/local/bolt/smlv_germline
 include { BOLT_SMLV_GERMLINE_REPORT  } from '../modules/local/bolt/smlv_germline/report/main'
 include { BOLT_SMLV_SOMATIC_ANNOTATE } from '../modules/local/bolt/smlv_somatic/annotate/main'
 include { BOLT_SMLV_SOMATIC_FILTER   } from '../modules/local/bolt/smlv_somatic/filter/main'
-include { BOLT_SMLV_SOMATIC_REPORT   } from '../modules/local/bolt/smlv_somatic/report/main'
 include { BOLT_SMLV_SOMATIC_RESCUE   } from '../modules/local/bolt/smlv_somatic/rescue/main'
+include { BOLT_SMLV_SOMATIC_REPORT   } from '../modules/local/bolt/smlv_somatic/report/main'
 include { BOLT_SV_SOMATIC_ANNOTATE   } from '../modules/local/bolt/sv_somatic/annotate/main'
 include { BOLT_SV_SOMATIC_PRIORITISE } from '../modules/local/bolt/sv_somatic/prioritise/main'
-include { ESVEE_CALL                 } from '../modules/local/esvee/call/main'
 include { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
+include { SIGRAP_HRDETECT            } from '../modules/local/sigrap/hrdetect/main'
+include { SIGRAP_MUTPAT              } from '../modules/local/sigrap/mutpat/main'
+include { VCF2MAF                    } from '../modules/local/vcf2maf/main'
+
 
+include { ESVEE_CALL                 } from '../modules/local/esvee/call/main'
 include { LINX_ANNOTATION            } from '../subworkflows/local/linx_annotation'
 include { LINX_PLOTTING              } from '../subworkflows/local/linx_plotting'
 include { PREPARE_INPUT              } from '../subworkflows/local/prepare_input'
@@ -74,13 +78,6 @@ workflow SASH {
     // channel: [ versions.yml ]
     ch_versions = Channel.empty()
 
-
-
-
-    //
-    // Prepare inputs from samplesheet
-    //
-
     PREPARE_INPUT(
         file(params.input),
     )
@@ -93,6 +90,7 @@ workflow SASH {
     ch_sage_somatic        = PREPARE_INPUT.out.sage_somatic      // channel: [ meta, sage_somatic_vcf, sage_somatic_tbi ]
     ch_virusbreakend       = PREPARE_INPUT.out.virusbreakend     // channel: [ meta, virusbreakend_dir ]
     ch_call_inputs         = PREPARE_INPUT.out.call_inputs       // channel: [ meta_esvee, esvee_ref_depth_vcf, esvee_prep_dir ]
+    ch_chord               = PREPARE_INPUT.out.chord             // channel: [ meta, chord_prediction_tsv ]
 
     // DRAGEN inputs
     ch_input_hrd           = PREPARE_INPUT.out.hrd               // channel: [ meta, hrdscore_csv ]
@@ -120,8 +118,7 @@ workflow SASH {
     // Somatic small variants
     //
 
-
-
+    // Prepare rescue inputs with meta transformation
     // channel: [ meta_bolt, dragen_somatic_vcf, dragen_somatic_tbi, sage_somatic_vcf, sage_somatic_tbi ]
     ch_smlv_somatic_rescue_inputs = WorkflowSash.groupByMeta(
         ch_input_vcf_somatic,
@@ -152,6 +149,7 @@ workflow SASH {
         umccr_data.annotations_dir,
         misc_data.pon_dir,
         misc_data.pcgr_dir,
+        misc_data.vep_dir
     )
 
     ch_versions = ch_versions.mix(BOLT_SMLV_SOMATIC_ANNOTATE.out.versions)
@@ -162,6 +160,7 @@ workflow SASH {
 
     ch_versions = ch_versions.mix(BOLT_SMLV_SOMATIC_FILTER.out.versions)
 
+    // Restore meta and create clean outputs
     // channel: [ meta, smlv_somatic_vcf ]
     ch_smlv_somatic_out = WorkflowSash.restoreMeta(BOLT_SMLV_SOMATIC_FILTER.out.vcf, ch_inputs)
         .map { meta, vcf, tbi -> [meta, vcf] }
@@ -181,12 +180,42 @@ workflow SASH {
         hmf_data.gnomad_resource,
     )
 
+    ch_versions = ch_versions.mix(PAVE_SOMATIC.out.versions)
+
     // channel: [ meta, pave_somatic_vcf ]
     ch_pave_somatic_out = WorkflowSash.restoreMeta(PAVE_SOMATIC.out.vcf, ch_inputs)
 
 
 
 
+    //
+    // Convert somatic VCF to MAF format
+    //
+
+    // channel: [ meta_vcf2maf, smlv_somatic_vcf ]
+    ch_vcf2maf_inputs = ch_smlv_somatic_out.map { meta, vcf ->
+        def meta_vcf2maf = [
+            key: meta.id,
+            id: meta.id,
+            tumor_id: meta.tumor_id,
+            normal_id: meta.normal_id,
+        ]
+        return [meta_vcf2maf, vcf]
+    }
+
+    VCF2MAF(
+        ch_vcf2maf_inputs,
+        genome.fasta
+    )
+
+    ch_versions = ch_versions.mix(VCF2MAF.out.versions)
+
+    // channel: [ meta, somatic_maf ]
+    ch_vcf2maf_out = VCF2MAF.out.maf
+
+
+
+
     //
     // Germline small variants
     //
@@ -219,7 +248,6 @@ workflow SASH {
 
     //
     // Somatic structural variants
-
     //
 
     ESVEE_CALL(
@@ -304,6 +332,7 @@ workflow SASH {
     BOLT_SMLV_SOMATIC_REPORT(
         ch_smlv_somatic_report_inputs,
         misc_data.pcgr_dir,
+        misc_data.vep_dir,
         umccr_data.somatic_panel_regions_cds,
         hmf_data.sage_highconf_regions,
         genome.fasta,
@@ -330,6 +359,7 @@ workflow SASH {
         ch_smlv_germline_report_inputs,
         umccr_data.germline_panel_genes,
         misc_data.pcgr_dir,
+        misc_data.vep_dir
     )
 
     ch_versions = ch_versions.mix(BOLT_SMLV_GERMLINE_REPORT.out.versions)
@@ -430,11 +460,60 @@ workflow SASH {
 
 
 
+    //
+    // Sigrap
+    //
+
+    // channel: [ meta_sigrap, smlv_somatic_vcf, sv_somatic_vcf, cnv_somatic_tsv ]
+    ch_sigrap_hrdetect_inputs = WorkflowSash.groupByMeta(
+        ch_smlv_somatic_out,
+        ch_sv_somatic_sv_vcf_out,
+        ch_sv_somatic_cnv_tsv_out,
+    )
+        .map { meta, smlv_vcf, sv_vcf, cnv_tsv ->
+            def meta_sigrap = [
+                key: meta.id,
+                id: meta.id,
+                tumor_id: meta.tumor_id,
+            ]
+            return [meta_sigrap, smlv_vcf, sv_vcf, cnv_tsv]
+        }
+
+    SIGRAP_HRDETECT(
+        ch_sigrap_hrdetect_inputs
+    )
+
+    // channel: [ meta, hrdetect_json ]
+    ch_sigrap_hrdetect = WorkflowSash.restoreMeta(SIGRAP_HRDETECT.out.hrdetect_json, ch_inputs)
+    ch_versions = ch_versions.mix(SIGRAP_HRDETECT.out.versions)
+
+    // channel: [ meta_sigrap, smlv_somatic_vcf ]
+    ch_sigrap_mutpat_inputs = ch_smlv_somatic_out.map { meta, vcf ->
+        def meta_sigrap = [
+            key: meta.id,
+            id: meta.id,
+            tumor_id: meta.tumor_id,
+        ]
+        return [meta_sigrap, vcf]
+    }
+
+    SIGRAP_MUTPAT(
+        ch_sigrap_mutpat_inputs
+    )
+
+    // channel: [ meta, mutpat_output ]
+    ch_sigrap_mutpat = WorkflowSash.restoreMeta(SIGRAP_MUTPAT.out.mutpat_output, ch_inputs)
+    ch_versions = ch_versions.mix(SIGRAP_MUTPAT.out.versions)
+
+
+
+
+
     //
     // Generate the cancer report
     //
 
-    // channel: [ meta_bolt, smlv_somatic_vcf, smlv_somatic_bcftools_stats, smlv_somatic_counts_process, sv_tsv, sv_vcf, cnv_tsv, af_global, af_keygenes, purple_baf_circos_plot, purple_dir, virusbreakend_dir, dragen_hrd ]
+    // channel: [ meta_bolt, smlv_somatic_vcf, smlv_somatic_bcftools_stats, smlv_somatic_counts_process, sv_tsv, sv_vcf, cnv_tsv, af_global, af_keygenes, purple_baf_circos_plot, purple_dir, virusbreakend_dir, dragen_hrd, mutpat, hrdetect, chord ]
     ch_cancer_report_inputs = WorkflowSash.groupByMeta(
         ch_smlv_somatic_out,
         ch_smlv_somatic_report_stats_out,
@@ -448,6 +527,9 @@ workflow SASH {
         PURPLE_CALLING.out.purple_dir,
         ch_virusbreakend,
         ch_input_hrd,
+        ch_sigrap_mutpat,
+        ch_sigrap_hrdetect,
+        ch_chord,
         flatten_mode: 'nonrecursive',
     )
         .map {
@@ -478,11 +560,11 @@ workflow SASH {
 
     // channel: [ meta, somatic_dragen_dir ]
     ch_input_dragen_somatic_dir = ch_inputs
-        .map { meta -> [meta, meta.dragen_somatic_dir] }
+        .map { meta -> [meta, file(meta.dragen_somatic_dir)] }
 
     // channel: [ meta, germline_dragen_dir ]
     ch_input_dragen_germline_dir = ch_inputs
-        .map { meta -> [meta, meta.dragen_germline_dir] }
+        .map { meta -> [meta, file(meta.dragen_germline_dir)] }
 
     // channel: [ meta_multiqc, [somatic_dragen_dir, germline_dragen_dir, somatic_bcftools_stats, germline_bcftools_stats, somatic_counts_type, germline_counts_type, purple_dir] ]
     ch_multiqc_report_inputs = WorkflowSash.groupByMeta(
@@ -518,7 +600,7 @@ workflow SASH {
 
 
     //
-    // Annotate post processed strucutral variant events
+    // Annotate post processed structural variant events
     //
 
     LINX_ANNOTATION(
@@ -542,7 +624,6 @@ workflow SASH {
 
 
 
-
     //
     // TASK: Aggregate software versions
     //