From ed9c127221d85c07bf67a0a0df3fc200a64c9f7e Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 9 Dec 2024 17:04:17 +1100
Subject: [PATCH 01/88] add sigrap modules

---
 modules/local/sigrap/chord/main.nf    | 39 ++++++++++++++++++++++++++
 modules/local/sigrap/hrdetect/main.nf | 40 +++++++++++++++++++++++++++
 modules/local/sigrap/mutpat/main.nf   | 38 +++++++++++++++++++++++++
 workflows/sash.nf                     |  4 +++
 4 files changed, 121 insertions(+)
 create mode 100644 modules/local/sigrap/chord/main.nf
 create mode 100644 modules/local/sigrap/hrdetect/main.nf
 create mode 100644 modules/local/sigrap/mutpat/main.nf

diff --git a/modules/local/sigrap/chord/main.nf b/modules/local/sigrap/chord/main.nf
new file mode 100644
index 00000000..f8b8b25e
--- /dev/null
+++ b/modules/local/sigrap/chord/main.nf
@@ -0,0 +1,39 @@
+process SIGRAP_CHORD {
+    tag "${meta.id}"
+    label 'process_low'
+
+    container 'docker.io/qclayssen/sigrap:0.1.1'
+
+    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)
+
+    output:
+    path 'output/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 chord \\
+        --sample ${meta.subject_id} \\
+        --snv ${smlv_somatic_vcf} \\
+        --sv ${sv_somatic_vcf} \\
+        --out  output/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sigrap: \$(sigrap --version | sed 's/^.*version //')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir -p output/
+    touch output/chord.json.gz
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
+    """
+}
diff --git a/modules/local/sigrap/hrdetect/main.nf b/modules/local/sigrap/hrdetect/main.nf
new file mode 100644
index 00000000..e02c2d4d
--- /dev/null
+++ b/modules/local/sigrap/hrdetect/main.nf
@@ -0,0 +1,40 @@
+process SIGRAP_HRDETECT {
+    tag "${meta.id}"
+    label 'process_low'
+
+    container 'docker.io/qclayssen/sigrap:0.1.1'
+
+    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)
+
+    output:
+    path 'output/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 hrdetect \\
+        --sample ${meta.subject_id} \\
+        --snv ${smlv_somatic_vcf} \\
+        --sv ${sv_somatic_vcf} \\
+        --cnv ${cnv_somatic_tsv} \\
+        --out  output/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sigrap: \$(sigrap --version | sed 's/^.*version //')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir -p output/
+    touch output/hrdetect.json.gz
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
+    """
+}
diff --git a/modules/local/sigrap/mutpat/main.nf b/modules/local/sigrap/mutpat/main.nf
new file mode 100644
index 00000000..ab2bb5ac
--- /dev/null
+++ b/modules/local/sigrap/mutpat/main.nf
@@ -0,0 +1,38 @@
+process SIGRAP_MUTPAT {
+    tag "${meta.id}"
+    label 'process_low'
+
+    container 'docker.io/qclayssen/sigrap:0.1.1'
+
+    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)
+
+    output:
+    path 'output/'                               , emit: mutpat_output
+    path 'versions.yml'                                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    sigrap mutpat \\
+        --sample ${meta.subject_id} \\
+        --snv ${smlv_somatic_vcf} \\
+        --out  output/
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sigrap: \$(sigrap --version | sed 's/^.*version //')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir -p output/
+    touch output/chord.json.gz
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
+    """
+}
diff --git a/workflows/sash.nf b/workflows/sash.nf
index b963867a..30e6edf4 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -47,6 +47,10 @@ include { BOLT_SMLV_SOMATIC_RESCUE   } from '../modules/local/bolt/smlv_somatic/
 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 { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
+include { SIGRAP_CHORD               } from '../modules/local/sigvrap/chord/main'
+include { SIGRAP_HRDETECT            } from '../modules/local/sigvrap/hrdetect/main'
+include { SIGRAP_MUTPAT              } from '../modules/local/sigvrap/mutpat/main'
+
 
 include { GRIPSS_FILTERING           } from '../subworkflows/local/gripss_filtering'
 include { LINX_ANNOTATION            } from '../subworkflows/local/linx_annotation'

From 8914f8e75698badd6e51208901265f39285ab13a Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 21 Feb 2025 09:45:10 +1100
Subject: [PATCH 02/88] changes images modules

---
 modules/local/bolt/other/cancer_report/main.nf | 2 +-
 modules/local/sigrap/chord/main.nf             | 5 +++--
 modules/local/sigrap/hrdetect/main.nf          | 2 +-
 modules/local/sigrap/mutpat/main.nf            | 4 ++--
 4 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index 4690eda8..3000f4f6 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/scwatts/bolt:0.2.13-gpgr'
+    container 'docker.io/qclayssen/bolt:gpgr-input-sigrap-data'
 
     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)
diff --git a/modules/local/sigrap/chord/main.nf b/modules/local/sigrap/chord/main.nf
index f8b8b25e..80199d2d 100644
--- a/modules/local/sigrap/chord/main.nf
+++ b/modules/local/sigrap/chord/main.nf
@@ -2,10 +2,11 @@ process SIGRAP_CHORD {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/sigrap:0.1.1'
+    container 'ghcr.io/umccr/sigrap:0.2.0'
 
     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)
+    tuple val(meta), path(sv_somatic_vcf)
 
     output:
     path 'output/chord.json.gz'                               , emit: chord_json
diff --git a/modules/local/sigrap/hrdetect/main.nf b/modules/local/sigrap/hrdetect/main.nf
index e02c2d4d..425819f6 100644
--- a/modules/local/sigrap/hrdetect/main.nf
+++ b/modules/local/sigrap/hrdetect/main.nf
@@ -2,7 +2,7 @@ process SIGRAP_HRDETECT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/sigrap:0.1.1'
+    container 'ghcr.io/umccr/sigrap:0.2.0'
 
     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)
diff --git a/modules/local/sigrap/mutpat/main.nf b/modules/local/sigrap/mutpat/main.nf
index ab2bb5ac..6173fc7d 100644
--- a/modules/local/sigrap/mutpat/main.nf
+++ b/modules/local/sigrap/mutpat/main.nf
@@ -2,13 +2,13 @@ process SIGRAP_MUTPAT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/sigrap:0.1.1'
+    container 'ghcr.io/umccr/sigrap:0.2.0'
 
     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)
 
     output:
-    path 'output/'                               , emit: mutpat_output
+    path 'output/'                                            , emit: mutpat_output
     path 'versions.yml'                                       , emit: versions
 
     when:

From 03c2cf337b337da4006f96523808307f6899b263 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 21 Feb 2025 09:46:01 +1100
Subject: [PATCH 03/88] uptade workflow with modules a channels

---
 workflows/sash.nf | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 30e6edf4..33c878cd 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -473,6 +473,21 @@ workflow SASH {
             return [meta, hrd]
         }
 
+    SIGRAP_CHORD(
+        ch_smlv_somatic_out,
+        ch_sv_somatic_sv_vcf_out
+    )
+    SIGRAP_HRDETECT(
+        ch_smlv_somatic_out,
+        ch_sv_somatic_sv_vcf_out,
+        ch_sv_somatic_cnv_tsv_out,
+
+
+    )
+    SIGRAP_MUTPAT(
+        ch_smlv_somatic_out
+    )
+
     // 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 ]
     ch_cancer_report_inputs = WorkflowSash.groupByMeta(
         ch_smlv_somatic_out,
@@ -487,6 +502,9 @@ workflow SASH {
         PURPLE_CALLING.out.purple_dir,
         ch_virusbreakend,
         ch_input_hrd,
+        SIGRAP_MUTPAT.out.mutpat_output,
+        SIGRAP_HRDETECT.out.hrdetect_json,
+        SIGRAP_CHORD.out.chord_json
     )
         .map {
             def meta = it[0]

From e8bf9d3a584bc4eac20b3d0bb575dcdad5f1ec5c Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 21 Feb 2025 16:34:11 +1100
Subject: [PATCH 04/88] fix typo

---
 workflows/sash.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 33c878cd..fe8d9b2f 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -47,9 +47,9 @@ include { BOLT_SMLV_SOMATIC_RESCUE   } from '../modules/local/bolt/smlv_somatic/
 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 { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
-include { SIGRAP_CHORD               } from '../modules/local/sigvrap/chord/main'
-include { SIGRAP_HRDETECT            } from '../modules/local/sigvrap/hrdetect/main'
-include { SIGRAP_MUTPAT              } from '../modules/local/sigvrap/mutpat/main'
+include { SIGRAP_CHORD               } from '../modules/local/sigrap/chord/main'
+include { SIGRAP_HRDETECT            } from '../modules/local/sigrap/hrdetect/main'
+include { SIGRAP_MUTPAT              } from '../modules/local/sigrap/mutpat/main'
 
 
 include { GRIPSS_FILTERING           } from '../subworkflows/local/gripss_filtering'

From ab0d3b910eaad0c281027e542bac5629ae004d20 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 21 Feb 2025 16:38:37 +1100
Subject: [PATCH 05/88] fix input module

---
 modules/local/sigrap/hrdetect/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/local/sigrap/hrdetect/main.nf b/modules/local/sigrap/hrdetect/main.nf
index 425819f6..1bc175d3 100644
--- a/modules/local/sigrap/hrdetect/main.nf
+++ b/modules/local/sigrap/hrdetect/main.nf
@@ -5,7 +5,9 @@ process SIGRAP_HRDETECT {
     container 'ghcr.io/umccr/sigrap:0.2.0'
 
     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)
+    path(smlv_somatic_vcf)
+    path(sv_somatic_vcf)
+    path(cnv_somatic_tsv)
 
     output:
     path 'output/hrdetect.json.gz'                            , emit: hrdetect_json

From 0011e478d73e5662b0b0a3783ee5ebec74950960 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 29 Apr 2025 14:16:15 +1000
Subject: [PATCH 06/88] replace gridss by esvee data

---
 workflows/sash.nf | 50 ++++++++++++++++++++---------------------------
 1 file changed, 21 insertions(+), 29 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index b963867a..a978f77f 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -95,14 +95,29 @@ workflow SASH {
     // channel: [ meta, cobalt_dir ]
     ch_cobalt = ch_inputs.map { meta -> [meta, file(meta.oncoanalyser_dir).toUriString() + '/cobalt/'] }
 
-    // channel: [ meta, gripss_somatic_vcf, gripss_somatic_tbi ]
-    ch_gridss = ch_inputs
+    // channel: [ meta, esvee_somatic_vcf, esvee_somatic_tbi ]
+    ch_esvee_somatic = ch_inputs
         .map { meta ->
-            def subpath = "/gridss/${meta.tumor_id}.gridss.vcf.gz"
+            def subpath = "/esvee/caller/${meta.tumor_id}.esvee.somatic.vcf.gz"
             def vcf = file(meta.oncoanalyser_dir).toUriString() + subpath
             return [meta, vcf]
         }
 
+    // channel: [ meta, esvee_germline_vcf, esvee_germline_tbi ]
+    ch_esvee_germline = ch_inputs
+        .map { meta ->
+            def subpath = "/esvee/caller/${meta.tumor_id}.esvee.germline.vcf.gz"
+            def vcf = file(meta.oncoanalyser_dir).toUriString() + subpath
+            return [meta, vcf]
+        }
+
+    // channel: [ meta, esvee_somatic_unfiltred_vcf, esvee_somatic_unfiltred_tbi ]
+    ch_esvee_somatic_unfiltred = ch_inputs
+        .map { meta ->
+            def subpath = "/esvee/caller/${meta.tumor_id}.esvee.unfiltered.vcf.g"
+            def vcf = file(meta.oncoanalyser_dir).toUriString() + subpath
+            return [meta, vcf]
+        }
     // channel: [ meta, sage_somatic_vcf, sage_somatic_tbi ]
     ch_sage_somatic = ch_inputs
         .map { meta ->
@@ -246,27 +261,6 @@ workflow SASH {
     ch_smlv_germline_out = WorkflowSash.restoreMeta(BOLT_SMLV_GERMLINE_PREPARE.out.vcf, ch_inputs)
 
 
-
-
-
-    //
-    // Somatic structural variants
-    //
-    GRIPSS_FILTERING(
-        ch_inputs,
-        ch_gridss,
-        genome.fasta,
-        genome.version,
-        genome.fai,
-        hmf_data.gridss_pon_breakends,
-        hmf_data.gridss_pon_breakpoints,
-        umccr_data.known_fusions,
-        hmf_data.repeatmasker_annotations,
-    )
-
-
-
-
     //
     // CNV calling using UMCCR postprocessed variants
     //
@@ -284,11 +278,9 @@ workflow SASH {
         //   * https://github.com/hartwigmedical/hmftools/blob/a2f82e5/purple/src/main/java/com/hartwig/hmftools/purple/germline/GermlineGenotypeEnrichment.java#L63
         //ch_smlv_germline_out,
         ch_smlv_germline_out.map { meta, vcf -> return [meta, []] },
-
-
-        GRIPSS_FILTERING.out.somatic,
-        GRIPSS_FILTERING.out.germline,
-        GRIPSS_FILTERING.out.somatic_unfiltered,
+        ch_esvee_somatic,
+        ch_esvee_germline,
+        ch_esvee_somatic_unfiltred,
         genome.fasta,
         genome.version,
         genome.fai,

From 9da48e7adfa4e1bfda0bf8e6c1cd3eb90f435203 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 30 Apr 2025 10:58:46 +1000
Subject: [PATCH 07/88] change input channel files in subworkflow

---
 subworkflows/local/prepare_input.nf | 57 ++++++++++++++++++++
 workflows/sash.nf                   | 81 +++++------------------------
 2 files changed, 70 insertions(+), 68 deletions(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 0e32f978..8ea361f8 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -40,6 +40,63 @@ workflow PREPARE_INPUT {
                 return meta
             }
 
+        // map oncoanalyser assets and DRAGEN outputs into channels
+        def ch_amber = ch_metas.map { meta ->
+            def base = file(meta.oncoanalyser_dir).toUriString()
+            return [meta, "${base}/amber/"]
+        }
+        def ch_cobalt = ch_metas.map { meta ->
+            def base = file(meta.oncoanalyser_dir).toUriString()
+            return [meta, "${base}/cobalt/"]
+        }
+        def ch_esvee_somatic = ch_metas.map { meta ->
+            def base = file(meta.oncoanalyser_dir).toUriString()
+            def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.somatic.vcf.gz"
+            return [meta, vcf]
+        }
+        def ch_esvee_germline = ch_metas.map { meta ->
+            def base = file(meta.oncoanalyser_dir).toUriString()
+            def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.germline.vcf.gz"
+            return [meta, vcf]
+        }
+        def ch_esvee_somatic_unfiltered = ch_metas.map { meta ->
+            def base = file(meta.oncoanalyser_dir).toUriString()
+            def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.unfiltered.vcf.gz"
+            return [meta, vcf]
+        }
+        def ch_sage_somatic = ch_metas.map { meta ->
+            def base = file(meta.oncoanalyser_dir).toUriString()
+            def vcf = "${base}/sage/somatic/${meta.tumor_id}.sage.somatic.vcf.gz"
+            return [meta, vcf, "${vcf}.tbi"]
+        }
+        def ch_virusbreakend = ch_metas.map { meta ->
+            def base = file(meta.oncoanalyser_dir).toUriString()
+            return [meta, "${base}/virusbreakend/"]
+        }
+        def ch_input_hrd = ch_metas.map { meta ->
+            def base = file(meta.dragen_somatic_dir).toUriString()
+            return [meta, "${base}/${meta.tumor_id}.hrdscore.csv"]
+        }
+        def ch_input_vcf_germline = ch_metas.map { meta ->
+            def base = file(meta.dragen_germline_dir).toUriString()
+            return [meta, "${base}/${meta.normal_id}.hard-filtered.vcf.gz"]
+        }
+        def ch_input_vcf_somatic = ch_metas.map { meta ->
+            def base = file(meta.dragen_somatic_dir).toUriString()
+            def vcf = "${base}/${meta.tumor_id}.hard-filtered.vcf.gz"
+            return [meta, vcf, "${vcf}.tbi"]
+        }
+
     emit:
         metas = ch_metas
+        amber = ch_amber
+        cobalt = ch_cobalt
+        esvee_somatic = ch_esvee_somatic
+        esvee_germline = ch_esvee_germline
+        esvee_somatic_unfiltered = ch_esvee_somatic_unfiltered
+        sage_somatic = ch_sage_somatic
+        virusbreakend = ch_virusbreakend
+        hrd = ch_input_hrd
+        vcf_germline = ch_input_vcf_germline
+        vcf_somatic = ch_input_vcf_somatic
 }
diff --git a/workflows/sash.nf b/workflows/sash.nf
index a978f77f..2336e5d2 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -87,52 +87,16 @@ workflow SASH {
     )
     ch_inputs = PREPARE_INPUT.out.metas
 
-    // TODO(SW): place into subworkflow; simplify with map of variable name -> subpath
-
-    // channel: [ meta, amber_dir ]
-    ch_amber = ch_inputs.map { meta -> [meta, file(meta.oncoanalyser_dir).toUriString() + '/amber/'] }
-
-    // channel: [ meta, cobalt_dir ]
-    ch_cobalt = ch_inputs.map { meta -> [meta, file(meta.oncoanalyser_dir).toUriString() + '/cobalt/'] }
-
-    // channel: [ meta, esvee_somatic_vcf, esvee_somatic_tbi ]
-    ch_esvee_somatic = ch_inputs
-        .map { meta ->
-            def subpath = "/esvee/caller/${meta.tumor_id}.esvee.somatic.vcf.gz"
-            def vcf = file(meta.oncoanalyser_dir).toUriString() + subpath
-            return [meta, vcf]
-        }
-
-    // channel: [ meta, esvee_germline_vcf, esvee_germline_tbi ]
-    ch_esvee_germline = ch_inputs
-        .map { meta ->
-            def subpath = "/esvee/caller/${meta.tumor_id}.esvee.germline.vcf.gz"
-            def vcf = file(meta.oncoanalyser_dir).toUriString() + subpath
-            return [meta, vcf]
-        }
-
-    // channel: [ meta, esvee_somatic_unfiltred_vcf, esvee_somatic_unfiltred_tbi ]
-    ch_esvee_somatic_unfiltred = ch_inputs
-        .map { meta ->
-            def subpath = "/esvee/caller/${meta.tumor_id}.esvee.unfiltered.vcf.g"
-            def vcf = file(meta.oncoanalyser_dir).toUriString() + subpath
-            return [meta, vcf]
-        }
-    // channel: [ meta, sage_somatic_vcf, sage_somatic_tbi ]
-    ch_sage_somatic = ch_inputs
-        .map { meta ->
-            def subpath = "/sage/somatic/${meta.tumor_id}.sage.somatic.vcf.gz"
-            def vcf = file(meta.oncoanalyser_dir).toUriString() + subpath
-            return [meta, vcf, "${vcf}.tbi"]
-        }
-
-    // channel: [ meta, virusbreakend_dir ]
-    ch_virusbreakend = ch_inputs
-        .map { meta ->
-            def subpath = '/virusbreakend/'
-            def virusbreakend_dir = file(meta.oncoanalyser_dir).toUriString() + subpath
-            return [meta, virusbreakend_dir]
-        }
+    ch_amber               = PREPARE_INPUT.out.amber
+    ch_cobalt              = PREPARE_INPUT.out.cobalt
+    ch_esvee_somatic       = PREPARE_INPUT.out.esvee_somatic
+    ch_esvee_germline      = PREPARE_INPUT.out.esvee_germline
+    ch_esvee_somatic_unfiltered = PREPARE_INPUT.out.esvee_somatic_unfiltered
+    ch_sage_somatic        = PREPARE_INPUT.out.sage_somatic
+    ch_virusbreakend       = PREPARE_INPUT.out.virusbreakend
+    ch_input_hrd          = PREPARE_INPUT.out.hrd
+    ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline
+    ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic
 
 
 
@@ -155,12 +119,6 @@ workflow SASH {
     // Somatic small variants
     //
 
-    // channel: [ meta, dragen_somatic_vcf, dragen_somatic_tbi ]
-    ch_input_vcf_somatic = ch_inputs
-        .map { meta ->
-            def vcf = file(meta.dragen_somatic_dir).toUriString() + "/${meta.tumor_id}.hard-filtered.vcf.gz"
-            return [meta, vcf, "${vcf}.tbi"]
-        }
 
 
     // channel: [ meta_bolt, dragen_somatic_vcf, dragen_somatic_tbi, sage_somatic_vcf, sage_somatic_tbi ]
@@ -176,7 +134,7 @@ workflow SASH {
                 tumor_id: meta.tumor_id,
                 normal_id: meta.normal_id,
             ]
-            return [meta_bolt, *it[1..-1]]
+            return [meta_bolt] + it[1..-1]
         }
 
     BOLT_SMLV_SOMATIC_RESCUE(
@@ -230,14 +188,6 @@ workflow SASH {
     // Germline small variants
     //
 
-    // channel: [ meta, dragen_germline_vcf ]
-    ch_input_vcf_germline = ch_inputs
-        .map { meta ->
-            def vcf = file(meta.dragen_germline_dir).toUriString() + "/${meta.normal_id}.hard-filtered.vcf.gz"
-            return [meta, vcf]
-        }
-
-    // channel: [ meta_bolt, dragen_germline_vcf ]
     ch_smlv_germline_prepare_inputs = ch_input_vcf_germline
         .map { meta, dragen_vcf ->
 
@@ -280,7 +230,7 @@ workflow SASH {
         ch_smlv_germline_out.map { meta, vcf -> return [meta, []] },
         ch_esvee_somatic,
         ch_esvee_germline,
-        ch_esvee_somatic_unfiltred,
+        ch_esvee_somatic_unfiltered,
         genome.fasta,
         genome.version,
         genome.fai,
@@ -455,11 +405,6 @@ workflow SASH {
     //
 
     // channel: [ meta, dragen_hrd ]
-    ch_input_hrd = ch_inputs
-        .map { meta ->
-            def hrd = file(meta.dragen_somatic_dir).toUriString() + "/${meta.tumor_id}.hrdscore.csv"
-            return [meta, 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 ]
     ch_cancer_report_inputs = WorkflowSash.groupByMeta(
@@ -484,7 +429,7 @@ workflow SASH {
                 subject_id: meta.subject_id,
                 tumor_id: meta.tumor_id,
             ]
-            return [meta_bolt, *it[1..-1]]
+            return [meta_bolt] + it[1..-1]
         }
 
     BOLT_OTHER_CANCER_REPORT(

From 033af833111568ba64d7d11cc2e870a314129291 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 30 Apr 2025 11:02:20 +1000
Subject: [PATCH 08/88] fix meta channel

---
 subworkflows/local/prepare_input.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 8ea361f8..802c92f8 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -3,7 +3,7 @@ workflow PREPARE_INPUT {
         ch_samplesheet
 
     main:
-        ch_metas = Channel.of(ch_samplesheet)
+        def ch_metas = Channel.of(ch_samplesheet)
             .splitCsv(header: true)
             .map { [it.id, it] }
             .groupTuple()

From c9136cf1da9564664f764fb4beed05de1fb67d98 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 30 Apr 2025 11:11:55 +1000
Subject: [PATCH 09/88] fix add tbi esvee files

---
 subworkflows/local/prepare_input.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 802c92f8..92c97af9 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -52,17 +52,17 @@ workflow PREPARE_INPUT {
         def ch_esvee_somatic = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.somatic.vcf.gz"
-            return [meta, vcf]
+            return [meta, vcf, "${vcf}.tbi"]
         }
         def ch_esvee_germline = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.germline.vcf.gz"
-            return [meta, vcf]
+            return [meta, vcf, "${vcf}.tbi"]
         }
         def ch_esvee_somatic_unfiltered = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.unfiltered.vcf.gz"
-            return [meta, vcf]
+            return [meta, vcf, "${vcf}.tbi"]
         }
         def ch_sage_somatic = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()

From 3e5399ae08b815f22e9abe48d136b83375c33b06 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 30 Apr 2025 14:27:21 +1000
Subject: [PATCH 10/88] add esvee module

---
 modules/local/esvee/call/environment.yml |  7 ++
 modules/local/esvee/call/main.nf         | 81 ++++++++++++++++++++++++
 modules/local/esvee/call/meta.yml        | 73 +++++++++++++++++++++
 3 files changed, 161 insertions(+)
 create mode 100644 modules/local/esvee/call/environment.yml
 create mode 100644 modules/local/esvee/call/main.nf
 create mode 100644 modules/local/esvee/call/meta.yml

diff --git a/modules/local/esvee/call/environment.yml b/modules/local/esvee/call/environment.yml
new file mode 100644
index 00000000..01355c11
--- /dev/null
+++ b/modules/local/esvee/call/environment.yml
@@ -0,0 +1,7 @@
+name: esvee_call
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hmftools-esvee=1.0.3
diff --git a/modules/local/esvee/call/main.nf b/modules/local/esvee/call/main.nf
new file mode 100644
index 00000000..a6480a18
--- /dev/null
+++ b/modules/local/esvee/call/main.nf
@@ -0,0 +1,81 @@
+process ESVEE_CALL {
+    tag "${meta.id}"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hmftools-esvee:1.0.3--hdfd78af_0' :
+        'biocontainers/hmftools-esvee:1.0.3--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(ref_depth_vcf), path(prep_dir)
+    path genome_fasta
+    val genome_ver
+    path pon_breakends
+    path pon_breakpoints
+    path known_fusions
+    path repeatmasker_annotations
+
+    output:
+    tuple val(meta), path("caller/")                                                                                                     , emit: caller_dir
+    tuple val(meta), path("caller/${meta.tumor_id}.esvee.unfiltered.vcf.gz"), path("caller/${meta.tumor_id}.esvee.unfiltered.vcf.gz.tbi"), emit: unfiltered_vcf
+    tuple val(meta), path("caller/${meta.tumor_id}.esvee.somatic.vcf.gz"),    path("caller/${meta.tumor_id}.esvee.somatic.vcf.gz.tbi")   , emit: somatic_vcf
+    tuple val(meta), path("caller/${meta.tumor_id}.esvee.germline.vcf.gz"),   path("caller/${meta.tumor_id}.esvee.germline.vcf.gz.tbi")  , emit: germline_vcf, optional: true
+    path 'versions.yml'                                                                                                                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    def xmx_mod = task.ext.xmx_mod ?: 0.95
+
+    def reference_arg = meta.normal_id != null ? "-reference ${meta.normal_id}" : ''
+
+    """
+    mkdir -p caller/
+
+    esvee com.hartwig.hmftools.esvee.caller.CallerApplication \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
+        ${args} \\
+        -sample ${meta.tumor_id} \\
+        ${reference_arg} \\
+        -input_vcf ${ref_depth_vcf} \\
+        -esvee_prep_dir ${prep_dir}/ \\
+        -ref_genome_version ${genome_ver} \\
+        -known_hotspot_file ${known_fusions} \\
+        -pon_sgl_file ${pon_breakends} \\
+        -pon_sv_file ${pon_breakpoints} \\
+        -repeat_mask_file ${repeatmasker_annotations} \\
+        -output_dir caller/ \\
+        -log_level DEBUG
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        esvee: \$(esvee -version | sed -n '/^Esvee version/ { s/^.* //p }')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir -p caller/
+
+    vcf_template='##fileformat=VCFv4.1
+    ##contig=<ID=.>
+    #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+    .	.	.	.	.	.	.
+    '
+
+    echo \${vcf_template} | gzip -c > caller/${meta.tumor_id}.esvee.unfiltered.vcf.gz
+    echo \${vcf_template} | gzip -c > caller/${meta.tumor_id}.esvee.somatic.vcf.gz
+
+    touch caller/${meta.tumor_id}.esvee.unfiltered.vcf.gz.tbi
+    touch caller/${meta.tumor_id}.esvee.somatic.vcf.gz.tbi
+
+    ${ (meta.normal_id != null) ? "touch caller/${meta.tumor_id}.esvee.germline.vcf.gz" : '' }
+    ${ (meta.normal_id != null) ? "touch caller/${meta.tumor_id}.esvee.germline.vcf.gz.tbi" : '' }
+
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
+    """
+}
diff --git a/modules/local/esvee/call/meta.yml b/modules/local/esvee/call/meta.yml
new file mode 100644
index 00000000..38979eb8
--- /dev/null
+++ b/modules/local/esvee/call/meta.yml
@@ -0,0 +1,73 @@
+name: esvee_call
+description: Call somatic SVs with ESVEE
+keywords:
+  - calling
+  - sv
+tools:
+  - esvee:
+      description: Structural variant (SV) calling
+      homepage: https://github.com/hartwigmedical/hmftools/tree/master/esvee
+      documentation: https://github.com/hartwigmedical/hmftools/tree/master/esvee
+      licence: ["GPL >=3"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [id: 'sample_id']
+  - ref_depth_vcf:
+      type: file
+      description: ESVEE depth annotated VCF file
+      pattern: "*.{vcf.gz}"
+  - prep_dir:
+      type: directory
+      description: ESVEE prep output directory
+  - genome_fasta:
+      type: file
+      description: Reference genome assembly FASTA file
+      pattern: "*.{fa,fasta}"
+  - genome_ver:
+      type: string
+      description: Reference genome version
+  - pon_breakend:
+      type: file
+      description: GRIDSS breakend PON file
+      pattern: "*.{bed.gz}"
+  - pon_breakpoints:
+      type: file
+      description: GRIDSS breakpoint PON file
+      pattern: "*.{bedpe.gz}"
+  - known_fusions:
+      type: file
+      description: HMF Known Fusions file
+      pattern: "*.{bedpe}"
+  - repeatmasker_annotations:
+      type: file
+      description: RepeatMasker annotations file
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [id: 'sample_id']
+  - caller_dir:
+      type: directory
+      description: ESVEE call output directory
+  - unfiltered_vcf:
+      type: list
+      description: Unfiltered VCF file
+      pattern: "*.{vcf.gz,vcf.gz.tbi}"
+  - somatic_vcf:
+      type: list
+      description: Somatic VCF file
+      pattern: "*.{vcf.gz,vcf.gz.tbi}"
+  - germline_vcf:
+      type: list
+      description: Germline VCF file (optional)
+      pattern: "*.{vcf.gz,vcf.gz.tbi}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@scwatts"

From 4e34cbe85e727a04c8034d0827b6623008946505 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 30 Apr 2025 14:27:35 +1000
Subject: [PATCH 11/88] update purple

---
 modules/local/purple/main.nf | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/modules/local/purple/main.nf b/modules/local/purple/main.nf
index 477d92ec..999e921b 100644
--- a/modules/local/purple/main.nf
+++ b/modules/local/purple/main.nf
@@ -1,8 +1,11 @@
 process PURPLE {
     tag "${meta.id}"
-    label 'process_low'
+    label 'process_medium'
 
-    container 'docker.io/scwatts/purple:4.0.2--1'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hmftools-purple:4.1--hdfd78af_0' :
+        'biocontainers/hmftools-purple:4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(amber), path(cobalt), path(sv_tumor_vcf), path(sv_tumor_tbi), path(sv_tumor_unfiltered_vcf), path(sv_tumor_unfiltered_tbi), path(sv_normal_vcf), path(sv_normal_tbi), path(smlv_tumor_vcf), path(smlv_normal_vcf)
@@ -30,6 +33,9 @@ process PURPLE {
     script:
     def args = task.ext.args ?: ''
 
+    // allow custom heap fraction
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def reference_arg = meta.containsKey('normal_id') ? "-reference ${meta.normal_id}" : ''
 
     def sv_tumor_vcf_arg = sv_tumor_vcf ? "-somatic_sv_vcf ${sv_tumor_vcf}" : ''
@@ -65,7 +71,7 @@ process PURPLE {
     fi;
 
     purple \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -tumor ${meta.tumor_id} \\
         ${reference_arg} \\
@@ -73,7 +79,6 @@ process PURPLE {
         -cobalt ${cobalt} \\
         ${sv_tumor_vcf_arg} \\
         ${sv_normal_vcf_arg} \\
-        ${sv_tumor_recovery_vcf_arg} \\
         ${smlv_tumor_vcf_arg} \\
         ${smlv_normal_vcf_arg} \\
         -ref_genome ${genome_fasta} \\
@@ -99,7 +104,7 @@ process PURPLE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        purple: \$(purple -version | sed 's/^.* //')
+        purple: \$(purple -version | sed -n '/^Purple version / { s/^.* //p }')
     END_VERSIONS
     """
 

From 7f2abbdd0ff31ae73ddcd18f46141756efa5c126 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 30 Apr 2025 15:01:01 +1000
Subject: [PATCH 12/88] fix image purple

---
 modules/local/purple/main.nf | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/modules/local/purple/main.nf b/modules/local/purple/main.nf
index 999e921b..706130eb 100644
--- a/modules/local/purple/main.nf
+++ b/modules/local/purple/main.nf
@@ -3,9 +3,7 @@ process PURPLE {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hmftools-purple:4.1--hdfd78af_0' :
-        'biocontainers/hmftools-purple:4.1--hdfd78af_0' }"
+    container 'docker.io/qclayssen/purple:4.1.0--1'
 
     input:
     tuple val(meta), path(amber), path(cobalt), path(sv_tumor_vcf), path(sv_tumor_tbi), path(sv_tumor_unfiltered_vcf), path(sv_tumor_unfiltered_tbi), path(sv_normal_vcf), path(sv_normal_tbi), path(smlv_tumor_vcf), path(smlv_normal_vcf)
@@ -79,6 +77,7 @@ process PURPLE {
         -cobalt ${cobalt} \\
         ${sv_tumor_vcf_arg} \\
         ${sv_normal_vcf_arg} \\
+        ${sv_tumor_recovery_vcf_arg} \\
         ${smlv_tumor_vcf_arg} \\
         ${smlv_normal_vcf_arg} \\
         -ref_genome ${genome_fasta} \\

From 6a2a0312c2e303474131b09ed904532c194762bf Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 30 Apr 2025 15:23:57 +1000
Subject: [PATCH 13/88] upgrade docker image and add env

---
 modules/local/linx/Dockerfile                 |  2 +-
 modules/local/linx/germline/environment.yml   |  7 +++
 modules/local/linx/germline/main.nf           |  9 ++-
 modules/local/linx/somatic/environment.yml    |  7 +++
 modules/local/linx/somatic/main.nf            | 13 +++--
 modules/local/linx/visualiser/environment.yml |  7 +++
 modules/local/linx/visualiser/main.nf         | 57 ++++++++++++++++---
 modules/local/linxreport/Dockerfile           |  2 +-
 modules/local/linxreport/environment.yml      |  7 +++
 modules/local/linxreport/main.nf              | 15 +++--
 modules/local/purple/Dockerfile               |  2 +-
 modules/local/purple/environment.yml          |  7 +++
 12 files changed, 110 insertions(+), 25 deletions(-)
 create mode 100644 modules/local/linx/germline/environment.yml
 create mode 100644 modules/local/linx/somatic/environment.yml
 create mode 100644 modules/local/linx/visualiser/environment.yml
 create mode 100644 modules/local/linxreport/environment.yml
 create mode 100644 modules/local/purple/environment.yml

diff --git a/modules/local/linx/Dockerfile b/modules/local/linx/Dockerfile
index eb57d724..bb54ea71 100644
--- a/modules/local/linx/Dockerfile
+++ b/modules/local/linx/Dockerfile
@@ -7,7 +7,7 @@ RUN \
     zlib && \
   micromamba clean --all --yes
 
-FROM quay.io/biocontainers/hmftools-linx:1.25--hdfd78af_0
+FROM quay.io/biocontainers/hmftools-linx:2.0--hdfd78af_0
 
 COPY --from=build /env/ /env/
 
diff --git a/modules/local/linx/germline/environment.yml b/modules/local/linx/germline/environment.yml
new file mode 100644
index 00000000..57471f2c
--- /dev/null
+++ b/modules/local/linx/germline/environment.yml
@@ -0,0 +1,7 @@
+name: linx_germline
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hmftools-linx=2.0
diff --git a/modules/local/linx/germline/main.nf b/modules/local/linx/germline/main.nf
index 8a5f4ac9..c3b436db 100644
--- a/modules/local/linx/germline/main.nf
+++ b/modules/local/linx/germline/main.nf
@@ -2,7 +2,7 @@ process LINX_GERMLINE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/scwatts/hmftools-linx:1.25--0'
+    container 'docker.io/qclayssen/hmftools-linx:2.0--10'
 
     input:
     tuple val(meta), path(sv_vcf)
@@ -20,9 +20,11 @@ process LINX_GERMLINE {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     linx \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -sv_vcf ${sv_vcf} \\
@@ -34,7 +36,7 @@ process LINX_GERMLINE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        linx: \$(linx -version | sed 's/^.* //')
+        linx: \$(linx -version | sed -n '/^Linx version / { s/^.* //p }')
     END_VERSIONS
     """
 
@@ -42,6 +44,7 @@ process LINX_GERMLINE {
     """
     mkdir linx_germline/
     touch linx_germline/placeholder
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/linx/somatic/environment.yml b/modules/local/linx/somatic/environment.yml
new file mode 100644
index 00000000..4d244fae
--- /dev/null
+++ b/modules/local/linx/somatic/environment.yml
@@ -0,0 +1,7 @@
+name: linx_somatic
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hmftools-linx=2.0
diff --git a/modules/local/linx/somatic/main.nf b/modules/local/linx/somatic/main.nf
index c0504829..e9d5426d 100644
--- a/modules/local/linx/somatic/main.nf
+++ b/modules/local/linx/somatic/main.nf
@@ -2,7 +2,7 @@ process LINX_SOMATIC {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/scwatts/hmftools-linx:1.25--0'
+    container 'docker.io/qclayssen/hmftools-linx:2.0--1'
 
     input:
     tuple val(meta), path(purple_dir)
@@ -10,7 +10,6 @@ process LINX_SOMATIC {
     path ensembl_data_resources
     path known_fusion_data
     path driver_gene_panel
-    path gene_id_file
 
     output:
     tuple val(meta), path('linx_somatic/'), emit: annotation_dir
@@ -21,26 +20,27 @@ process LINX_SOMATIC {
 
     script:
     def args = task.ext.args ?: ''
-    def gene_id_file_arg = gene_id_file ? "-gene_id_file ${gene_id_file}" : ''
+
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
 
     """
     linx \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -sv_vcf ${purple_dir}/${meta.sample_id}.purple.sv.vcf.gz \\
         -purple_dir ${purple_dir} \\
-        ${gene_id_file_arg} \\
         -ref_genome_version ${genome_ver} \\
         -ensembl_data_dir ${ensembl_data_resources} \\
         -known_fusion_file ${known_fusion_data} \\
         -driver_gene_panel ${driver_gene_panel} \\
         -write_vis_data \\
+        -write_neo_epitopes \\
         -output_dir linx_somatic/
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        linx: \$(linx -version | sed 's/^.* //')
+        linx: \$(linx -version | sed -n '/^Linx version / { s/^.* //p }')
     END_VERSIONS
     """
 
@@ -48,6 +48,7 @@ process LINX_SOMATIC {
     """
     mkdir linx_somatic/
     touch linx_somatic/placeholder
+
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/modules/local/linx/visualiser/environment.yml b/modules/local/linx/visualiser/environment.yml
new file mode 100644
index 00000000..5dadb70e
--- /dev/null
+++ b/modules/local/linx/visualiser/environment.yml
@@ -0,0 +1,7 @@
+name: linx_visualiser
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hmftools-linx=2.0
diff --git a/modules/local/linx/visualiser/main.nf b/modules/local/linx/visualiser/main.nf
index 01e28f2e..a40646a3 100644
--- a/modules/local/linx/visualiser/main.nf
+++ b/modules/local/linx/visualiser/main.nf
@@ -2,7 +2,7 @@ process LINX_VISUALISER {
     tag "${meta.id}"
     label 'process_medium'
 
-    container 'docker.io/scwatts/hmftools-linx:1.25--0'
+    container 'docker.io/qclayssen/hmftools-linx:2.0--1'
 
     input:
     tuple val(meta), path(linx_annotation_dir)
@@ -18,8 +18,19 @@ process LINX_VISUALISER {
 
     script:
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
 
     """
+    # NOTE(SW): the output plot directories are always required for ORANGE, which is straightfoward to handle with POSIX
+    # fs but more involved with FusionFS since it will not write empty directories to S3. A placeholder file can't be
+    # used in the plot directory to force FusionFS to create the directory as ORANGE will treat the placeholder as a PNG
+    # and fail. Optional outputs are possible but requires further channel logic and output to detect when complete.
+    # Instead I place the two plot output directories under a parent directory, only operating on that to allow use of a
+    # placeholder and support empty outputs when using FusionFS. Handling missing/non-existent directories are deferred
+    # to downstream processes, bypassing the need to implement further channel operations.
+
     mkdir -p plots/
 
     # NOTE(SW): LINX v1.24.1 require trailing slashes for the -plot_out and -data_out arguments since no filesystem
@@ -28,8 +39,10 @@ process LINX_VISUALISER {
     # https://github.com/hartwigmedical/hmftools/blob/linx-v1.24.1/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/ChromosomeRangeExecution.java#L22-L29
     # https://github.com/hartwigmedical/hmftools/blob/linx-v1.24.1/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/circos/FusionExecution.java#L18-L23
 
+    # Generate all chromosome and cluster plots by default
+
     linx \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         com.hartwig.hmftools.linx.visualiser.SvVisualiser \\
         ${args} \\
         -sample ${meta.sample_id} \\
@@ -38,19 +51,49 @@ process LINX_VISUALISER {
         -ensembl_data_dir ${ensembl_data_resources} \\
         -circos \$(which circos) \\
         -threads ${task.cpus} \\
-        -plot_out plots/ \\
-        -data_out data/
+        -plot_out plots/all/ \\
+        -data_out data/all/
+
+    # Rerun LINX to render only reportable cluster plots in a separate directory. While this is regenerating existing
+    # cluster plots, the number of reportable plots is generally very small and I prefer to rely on the internal LINX
+    # logic to determine whether a cluster is reportable rather than attempting to infer manually to copy out target
+    # plot files.
+
+    # The ORANGE report receives only reportable clusters while the gpgr LINX report receives chromosome and all cluster
+    # plots.
+
+    # https://github.com/hartwigmedical/hmftools/blob/linx-v1.24.1/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SampleData.java#L220-L236
+
+    linx \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
+        com.hartwig.hmftools.linx.visualiser.SvVisualiser \\
+        ${args2} \\
+        -sample ${meta.sample_id} \\
+        -vis_file_dir ${linx_annotation_dir} \\
+        -ref_genome_version ${genome_ver} \\
+        -ensembl_data_dir ${ensembl_data_resources} \\
+        -circos \$(which circos) \\
+        -plot_reportable \\
+        -threads ${task.cpus} \\
+        -plot_out plots/reportable/ \\
+        -data_out data/reportable/
+
+    # Create placeholders to force FusionFS to create parent plot directory on S3
+    if [[ \$(ls plots/ | wc -l) -eq 0 ]]; then
+        touch plots/.keep;
+    fi;
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        linx: \$(linx -version | sed 's/^.* //')
+        linx: \$(linx -version | sed -n '/^Linx version / { s/^.* //p }')
     END_VERSIONS
     """
 
     stub:
     """
-    mkdir -p plots/
-    touch plots/placeholder
+    mkdir -p plots/{all,reportable}/
+    touch plots/{all,reportable}/placeholder
+
     echo -e '${task.process}:\n  stub: noversions\n' > versions.yml
     """
 }
diff --git a/modules/local/linxreport/Dockerfile b/modules/local/linxreport/Dockerfile
index 963f2f5d..60850abb 100644
--- a/modules/local/linxreport/Dockerfile
+++ b/modules/local/linxreport/Dockerfile
@@ -7,7 +7,7 @@ RUN \
     zlib && \
   micromamba clean --all --yes
 
-FROM quay.io/biocontainers/r-linxreport:1.0.0--r43hdfd78af_0
+FROM quay.io/biocontainers/r-linxreport:1.1.0--r44hdfd78af_0
 
 COPY --from=build /env/ /env/
 
diff --git a/modules/local/linxreport/environment.yml b/modules/local/linxreport/environment.yml
new file mode 100644
index 00000000..71113340
--- /dev/null
+++ b/modules/local/linxreport/environment.yml
@@ -0,0 +1,7 @@
+name: linxreport
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::r-linxreport=1.1.0
diff --git a/modules/local/linxreport/main.nf b/modules/local/linxreport/main.nf
index fc28fcfd..4b9ab63a 100644
--- a/modules/local/linxreport/main.nf
+++ b/modules/local/linxreport/main.nf
@@ -2,7 +2,7 @@ process LINXREPORT {
     tag "${meta.id}"
     label 'process_single'
 
-    container 'docker.io/scwatts/r-linxreport:1.0.0--0'
+    container 'docker.io/scwatts/r-linxreport:1.1.0--0'
 
     input:
     tuple val(meta), path(linx_annotation_dir), path(linx_visualiser_dir)
@@ -17,22 +17,24 @@ process LINXREPORT {
     script:
     def args = task.ext.args ?: ''
 
+    def plot_dir = linx_visualiser_dir.resolve('all/').toUriString()
+
     """
-    # Create input directory if it doesn't exist for linxreport
-    if [[ ! -e ${linx_visualiser_dir} ]]; then
-        mkdir -p ${linx_visualiser_dir};
+    # Set input plot directory and create it doesn't exist. See the LINX visualiser module for further info.
+    if [[ ! -e ${plot_dir} ]]; then
+        mkdir -p ${plot_dir};
     fi;
 
     linxreport.R \\
         ${args} \\
         --sample ${meta.sample_id} \\
-        --plot ${linx_visualiser_dir} \\
+        --plot ${plot_dir} \\
         --table ${linx_annotation_dir} \\
         --out ${meta.sample_id}_linx.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        R: \$(R --version | head -n1 | sed 's/^R version \\([0-9.]\\+\\).\\+/\\1/')
+        r: \$(R --version | head -n1 | sed 's/^R version \\([0-9.]\\+\\).\\+/\\1/')
         linxreport: \$(linxreport.R --version)
     END_VERSIONS
     """
@@ -40,6 +42,7 @@ process LINXREPORT {
     stub:
     """
     touch ${meta.sample_id}_linx.html
+
     echo -e '${task.process}:\n  stub: noversions\n' > versions.yml
     """
 }
diff --git a/modules/local/purple/Dockerfile b/modules/local/purple/Dockerfile
index 26879a24..1cda1921 100644
--- a/modules/local/purple/Dockerfile
+++ b/modules/local/purple/Dockerfile
@@ -7,7 +7,7 @@ RUN \
     zlib && \
   micromamba clean --all --yes
 
-FROM quay.io/biocontainers/hmftools-purple:4.0.2--hdfd78af_0
+FROM quay.io/biocontainers/hmftools-purple:4.1--hdfd78af_0
 
 # NOTE(SW): copy over compatibile build of BCFtools
 COPY --from=quay.io/biocontainers/bcftools:1.19--h8b25389_0 /usr/local/ /usr/local/
diff --git a/modules/local/purple/environment.yml b/modules/local/purple/environment.yml
new file mode 100644
index 00000000..fb18f1e6
--- /dev/null
+++ b/modules/local/purple/environment.yml
@@ -0,0 +1,7 @@
+name: purple
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::hmftools-purple=4.1

From ab5a21034736a36a926abfe49526a9c724304ac9 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 30 Apr 2025 16:32:16 +1000
Subject: [PATCH 14/88] fix linx somatic

---
 modules/local/linx/somatic/main.nf | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/modules/local/linx/somatic/main.nf b/modules/local/linx/somatic/main.nf
index e9d5426d..c6d7041d 100644
--- a/modules/local/linx/somatic/main.nf
+++ b/modules/local/linx/somatic/main.nf
@@ -10,6 +10,8 @@ process LINX_SOMATIC {
     path ensembl_data_resources
     path known_fusion_data
     path driver_gene_panel
+    path gene_id_file
+
 
     output:
     tuple val(meta), path('linx_somatic/'), emit: annotation_dir
@@ -20,6 +22,8 @@ process LINX_SOMATIC {
 
     script:
     def args = task.ext.args ?: ''
+    def gene_id_file_arg = gene_id_file ? "-gene_id_file ${gene_id_file}" : ''
+
 
     def xmx_mod = task.ext.xmx_mod ?: 0.75
 
@@ -30,6 +34,7 @@ process LINX_SOMATIC {
         -sample ${meta.sample_id} \\
         -sv_vcf ${purple_dir}/${meta.sample_id}.purple.sv.vcf.gz \\
         -purple_dir ${purple_dir} \\
+        ${gene_id_file_arg} \\
         -ref_genome_version ${genome_ver} \\
         -ensembl_data_dir ${ensembl_data_resources} \\
         -known_fusion_file ${known_fusion_data} \\

From cd22e5ec3644944bb30e09f209152c815f9c6301 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 1 May 2025 11:40:48 +1000
Subject: [PATCH 15/88] fix purple input doesn't take sv_tumor_unfiltered_vcf

---
 modules/local/purple/main.nf | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/modules/local/purple/main.nf b/modules/local/purple/main.nf
index 706130eb..f267b00c 100644
--- a/modules/local/purple/main.nf
+++ b/modules/local/purple/main.nf
@@ -39,8 +39,6 @@ process PURPLE {
     def sv_tumor_vcf_arg = sv_tumor_vcf ? "-somatic_sv_vcf ${sv_tumor_vcf}" : ''
     def sv_normal_vcf_arg = sv_normal_vcf ? "-germline_sv_vcf ${sv_normal_vcf}" : ''
 
-    def sv_tumor_recovery_vcf_arg = sv_tumor_unfiltered_vcf ? "-sv_recovery_vcf ${sv_tumor_unfiltered_vcf}" : ''
-
     // NOTE(SW): use of 'smlv_tumor.vcf.gz' is intended here; see comment below in script block
     def smlv_tumor_vcf_arg = smlv_tumor_vcf ? "-somatic_vcf smlv_tumor.vcf.gz" : ''
     def smlv_normal_vcf_arg = smlv_normal_vcf ? "-germline_vcf ${smlv_normal_vcf}" : ''
@@ -77,7 +75,6 @@ process PURPLE {
         -cobalt ${cobalt} \\
         ${sv_tumor_vcf_arg} \\
         ${sv_normal_vcf_arg} \\
-        ${sv_tumor_recovery_vcf_arg} \\
         ${smlv_tumor_vcf_arg} \\
         ${smlv_normal_vcf_arg} \\
         -ref_genome ${genome_fasta} \\

From a0a2bbdb1f857ac318673f9effff077a9a4d0a23 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 1 May 2025 15:30:49 +1000
Subject: [PATCH 16/88] change dicker image bolt

---
 modules/local/bolt/sv_somatic/prioritise/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/bolt/sv_somatic/prioritise/main.nf b/modules/local/bolt/sv_somatic/prioritise/main.nf
index d2c0b7e9..4ac07c7e 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/scwatts/bolt:0.2.13'
+    container 'docker.io/qclayssen/bolt:oncoanalyser-v2'
 
     input:
     tuple val(meta), path(sv_vcf)

From 736c478ab0e39ea2c4f59be67f8b66e51037d59b Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 1 May 2025 15:52:55 +1000
Subject: [PATCH 17/88] fix docker path

---
 modules/local/linx/germline/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/linx/germline/main.nf b/modules/local/linx/germline/main.nf
index c3b436db..88c8c56e 100644
--- a/modules/local/linx/germline/main.nf
+++ b/modules/local/linx/germline/main.nf
@@ -2,7 +2,7 @@ process LINX_GERMLINE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/hmftools-linx:2.0--10'
+    container 'docker.io/qclayssen/hmftools-linx:2.0--1'
 
     input:
     tuple val(meta), path(sv_vcf)

From 48a153c244eeb124e1c00b266d925b05329f1c3c Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 1 May 2025 15:59:48 +1000
Subject: [PATCH 18/88] chane docker path linx report

---
 modules/local/linxreport/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/linxreport/main.nf b/modules/local/linxreport/main.nf
index 4b9ab63a..957407c1 100644
--- a/modules/local/linxreport/main.nf
+++ b/modules/local/linxreport/main.nf
@@ -2,7 +2,7 @@ process LINXREPORT {
     tag "${meta.id}"
     label 'process_single'
 
-    container 'docker.io/scwatts/r-linxreport:1.1.0--0'
+    container 'docker.io/qclayssen/r-linxreport:1.1.0--0'
 
     input:
     tuple val(meta), path(linx_annotation_dir), path(linx_visualiser_dir)

From af2e69c6077b94838212dba87c74c9b3a6c9a554 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 5 May 2025 09:42:44 +1000
Subject: [PATCH 19/88] change add eSVee call

---
 conf/modules.config                 |  8 +++++++
 subworkflows/local/prepare_input.nf | 22 +++++++------------
 workflows/sash.nf                   | 33 ++++++++++++++++++++++++-----
 3 files changed, 44 insertions(+), 19 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 04c86aec..da15bd78 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -171,6 +171,14 @@ process {
         ]
     }
 
+    withName: 'ESVEE_CALL' {
+        publishDir = [
+            path: { "${params.outdir}/esvee/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/esvee/${filename}" }
+        ]
+    }
+
     withName: '.*:LINX_ANNOTATION:(?:GERMLINE|SOMATIC)|.*:LINX_PLOTTING:VISUALISER' {
         ext.jarPath = '/opt/linx/linx.jar'
     }
diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 92c97af9..8c46a015 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -49,21 +49,17 @@ workflow PREPARE_INPUT {
             def base = file(meta.oncoanalyser_dir).toUriString()
             return [meta, "${base}/cobalt/"]
         }
-        def ch_esvee_somatic = ch_metas.map { meta ->
+        def ref_depth_vcf = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
-            def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.somatic.vcf.gz"
+            def vcf = "${base}/esvee/depth_annotation/${meta.tumor_id}.esvee.ref_depth.vcf.gz"
             return [meta, vcf, "${vcf}.tbi"]
         }
-        def ch_esvee_germline = ch_metas.map { meta ->
+        def prep_dir = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
-            def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.germline.vcf.gz"
-            return [meta, vcf, "${vcf}.tbi"]
-        }
-        def ch_esvee_somatic_unfiltered = ch_metas.map { meta ->
-            def base = file(meta.oncoanalyser_dir).toUriString()
-            def vcf = "${base}/esvee/caller/${meta.tumor_id}.esvee.unfiltered.vcf.gz"
-            return [meta, vcf, "${vcf}.tbi"]
+            def dir = "${base}/esvee/prep/"
+            return [meta, dir]
         }
+
         def ch_sage_somatic = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def vcf = "${base}/sage/somatic/${meta.tumor_id}.sage.somatic.vcf.gz"
@@ -86,17 +82,15 @@ workflow PREPARE_INPUT {
             def vcf = "${base}/${meta.tumor_id}.hard-filtered.vcf.gz"
             return [meta, vcf, "${vcf}.tbi"]
         }
-
     emit:
         metas = ch_metas
         amber = ch_amber
         cobalt = ch_cobalt
-        esvee_somatic = ch_esvee_somatic
-        esvee_germline = ch_esvee_germline
-        esvee_somatic_unfiltered = ch_esvee_somatic_unfiltered
         sage_somatic = ch_sage_somatic
         virusbreakend = ch_virusbreakend
         hrd = ch_input_hrd
         vcf_germline = ch_input_vcf_germline
         vcf_somatic = ch_input_vcf_somatic
+        ref_depth_vcf = ref_depth_vcf
+        prep_dir = prep_dir
 }
diff --git a/workflows/sash.nf b/workflows/sash.nf
index 2336e5d2..50844365 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -47,8 +47,8 @@ include { BOLT_SMLV_SOMATIC_RESCUE   } from '../modules/local/bolt/smlv_somatic/
 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 { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
+include { ESVEE_CALL                 } from '../modules/local/esvee/call/main'
 
-include { GRIPSS_FILTERING           } from '../subworkflows/local/gripss_filtering'
 include { LINX_ANNOTATION            } from '../subworkflows/local/linx_annotation'
 include { LINX_PLOTTING              } from '../subworkflows/local/linx_plotting'
 include { PREPARE_INPUT              } from '../subworkflows/local/prepare_input'
@@ -89,14 +89,13 @@ workflow SASH {
 
     ch_amber               = PREPARE_INPUT.out.amber
     ch_cobalt              = PREPARE_INPUT.out.cobalt
-    ch_esvee_somatic       = PREPARE_INPUT.out.esvee_somatic
-    ch_esvee_germline      = PREPARE_INPUT.out.esvee_germline
-    ch_esvee_somatic_unfiltered = PREPARE_INPUT.out.esvee_somatic_unfiltered
     ch_sage_somatic        = PREPARE_INPUT.out.sage_somatic
     ch_virusbreakend       = PREPARE_INPUT.out.virusbreakend
     ch_input_hrd          = PREPARE_INPUT.out.hrd
     ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline
     ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic
+    ch_ref_depth_vcf = PREPARE_INPUT.out.ref_depth_vcf
+    ch_prep_dir = PREPARE_INPUT.out.prep_dir
 
 
 
@@ -243,8 +242,33 @@ workflow SASH {
         hmf_data.purple_germline_del,
     )
 
+    //
+    // Somatic structural variants
+
+    //
+    // MODULE: ESVEE call somatic structural variants
+    //
+    // Create process input channel
+    // channel: [meta_esvee, ref_depth_vcf, prep_dir]
+    ch_call_inputs = WorkflowOncoanalyser.groupByMeta(
+        ch_ref_depth_vcf,
+        ch_prep_dir,
+    )
 
+    //TODO update ref data
+    ESVEE_CALL(
+        ch_call_inputs,
+        genome.fasta,
+        genome.version,
+        hmf_data.gridss_pon_breakends,
+        hmf_data.gridss_pon_breakpoints,
+        umccr_data.known_fusions,
+        hmf_data.repeatmasker_annotations,
+    )
 
+    ch_esvee_somatic       = ESVEE_CALL.out.somatic_vcf
+    ch_esvee_germline      = ESVEE_CALL.out.germline_vcf
+    ch_esvee_somatic_unfiltered = ESVEE_CALL.out.unfiltered_vcf
 
     //
     // Small variant reporting (PCGR, CPSR, stats)
@@ -370,7 +394,6 @@ workflow SASH {
 
 
 
-
     //
     // Generate custom PURPLE β-allele frequency circos plot
     //

From 4492f569d29e6a8a518d9582f6cd33d777807f7d Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 6 May 2025 17:05:43 +1000
Subject: [PATCH 20/88] fix name channel

---
 subworkflows/local/prepare_input.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 8c46a015..6d1e9eba 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -49,12 +49,12 @@ workflow PREPARE_INPUT {
             def base = file(meta.oncoanalyser_dir).toUriString()
             return [meta, "${base}/cobalt/"]
         }
-        def ref_depth_vcf = ch_metas.map { meta ->
+        def ch_ref_depth_vcf = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def vcf = "${base}/esvee/depth_annotation/${meta.tumor_id}.esvee.ref_depth.vcf.gz"
             return [meta, vcf, "${vcf}.tbi"]
         }
-        def prep_dir = ch_metas.map { meta ->
+        def chprep_dir = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def dir = "${base}/esvee/prep/"
             return [meta, dir]
@@ -91,6 +91,6 @@ workflow PREPARE_INPUT {
         hrd = ch_input_hrd
         vcf_germline = ch_input_vcf_germline
         vcf_somatic = ch_input_vcf_somatic
-        ref_depth_vcf = ref_depth_vcf
-        prep_dir = prep_dir
+        ref_depth_vcf = ch_ref_depth_vcf
+        prep_dir = ch_prep_dir
 }

From c084de20112f40a001dad86ddb93a52698135304 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 6 May 2025 17:09:35 +1000
Subject: [PATCH 21/88] fix typo

---
 subworkflows/local/prepare_input.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 6d1e9eba..8002a969 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -54,7 +54,7 @@ workflow PREPARE_INPUT {
             def vcf = "${base}/esvee/depth_annotation/${meta.tumor_id}.esvee.ref_depth.vcf.gz"
             return [meta, vcf, "${vcf}.tbi"]
         }
-        def chprep_dir = ch_metas.map { meta ->
+        def ch_prep_dir = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def dir = "${base}/esvee/prep/"
             return [meta, dir]

From d27f6ee5920c5b137792121e839c61eb4d7beff1 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 6 May 2025 17:16:23 +1000
Subject: [PATCH 22/88] fix fonction call

---
 workflows/sash.nf | 55 +++++++++++++++++++++++------------------------
 1 file changed, 27 insertions(+), 28 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 50844365..fdafe4a6 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -209,6 +209,33 @@ workflow SASH {
     // channel: [ meta, smlv_germline_vcf ]
     ch_smlv_germline_out = WorkflowSash.restoreMeta(BOLT_SMLV_GERMLINE_PREPARE.out.vcf, ch_inputs)
 
+    //
+    // Somatic structural variants
+
+    //
+    // MODULE: ESVEE call somatic structural variants
+    //
+    // Create process input channel
+    // channel: [meta_esvee, ref_depth_vcf, prep_dir]
+    ch_call_inputs = WorkflowSash.groupByMeta(
+        ch_ref_depth_vcf,
+        ch_prep_dir,
+    )
+
+    //TODO update ref data
+    ESVEE_CALL(
+        ch_call_inputs,
+        genome.fasta,
+        genome.version,
+        hmf_data.gridss_pon_breakends,
+        hmf_data.gridss_pon_breakpoints,
+        umccr_data.known_fusions,
+        hmf_data.repeatmasker_annotations,
+    )
+
+    ch_esvee_somatic       = ESVEE_CALL.out.somatic_vcf
+    ch_esvee_germline      = ESVEE_CALL.out.germline_vcf
+    ch_esvee_somatic_unfiltered = ESVEE_CALL.out.unfiltered_vcf
 
     //
     // CNV calling using UMCCR postprocessed variants
@@ -242,34 +269,6 @@ workflow SASH {
         hmf_data.purple_germline_del,
     )
 
-    //
-    // Somatic structural variants
-
-    //
-    // MODULE: ESVEE call somatic structural variants
-    //
-    // Create process input channel
-    // channel: [meta_esvee, ref_depth_vcf, prep_dir]
-    ch_call_inputs = WorkflowOncoanalyser.groupByMeta(
-        ch_ref_depth_vcf,
-        ch_prep_dir,
-    )
-
-    //TODO update ref data
-    ESVEE_CALL(
-        ch_call_inputs,
-        genome.fasta,
-        genome.version,
-        hmf_data.gridss_pon_breakends,
-        hmf_data.gridss_pon_breakpoints,
-        umccr_data.known_fusions,
-        hmf_data.repeatmasker_annotations,
-    )
-
-    ch_esvee_somatic       = ESVEE_CALL.out.somatic_vcf
-    ch_esvee_germline      = ESVEE_CALL.out.germline_vcf
-    ch_esvee_somatic_unfiltered = ESVEE_CALL.out.unfiltered_vcf
-
     //
     // Small variant reporting (PCGR, CPSR, stats)
     //

From 1d239057d38016a68b552877c06ecaaa2ba09397 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 6 May 2025 17:38:23 +1000
Subject: [PATCH 23/88] remove index esvee channel

---
 subworkflows/local/prepare_input.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 8002a969..d9cdbc6d 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -52,7 +52,7 @@ workflow PREPARE_INPUT {
         def ch_ref_depth_vcf = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def vcf = "${base}/esvee/depth_annotation/${meta.tumor_id}.esvee.ref_depth.vcf.gz"
-            return [meta, vcf, "${vcf}.tbi"]
+            return [meta, vcf]
         }
         def ch_prep_dir = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()

From ae3becdfa40b1c5c0dfa90e01c7f6514ebaa6d83 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 7 May 2025 09:09:30 +1000
Subject: [PATCH 24/88] add dockerfile eSVee

---
 modules/local/esvee/call/Dockerfile | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 modules/local/esvee/call/Dockerfile

diff --git a/modules/local/esvee/call/Dockerfile b/modules/local/esvee/call/Dockerfile
new file mode 100644
index 00000000..bd0796ca
--- /dev/null
+++ b/modules/local/esvee/call/Dockerfile
@@ -0,0 +1,15 @@
+FROM mambaorg/micromamba:1.5.7 as build
+
+USER root
+
+RUN \
+  micromamba create -y -p /env/ -c bioconda -c conda-forge \
+    zlib && \
+  micromamba clean --all --yes
+
+FROM quay.io/biocontainers/hmftools-esvee:1.0.3--hdfd78af_0
+
+COPY --from=build /env/ /env/
+
+ENV PATH="/env/bin:${PATH}"
+ENV LD_LIBRARY_PATH="/env/lib/:${LD_LIBRARY_PATH}"

From 015d5ab8d27ffd3e9d1f66ee21b53cc3174507eb Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 7 May 2025 09:14:26 +1000
Subject: [PATCH 25/88] change container esvee

---
 modules/local/esvee/call/main.nf | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/modules/local/esvee/call/main.nf b/modules/local/esvee/call/main.nf
index a6480a18..1447e79c 100644
--- a/modules/local/esvee/call/main.nf
+++ b/modules/local/esvee/call/main.nf
@@ -2,10 +2,8 @@ process ESVEE_CALL {
     tag "${meta.id}"
     label 'process_high'
 
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hmftools-esvee:1.0.3--hdfd78af_0' :
-        'biocontainers/hmftools-esvee:1.0.3--hdfd78af_0' }"
+    container 'docker.io/qclayssen/esvee:1.0.3'
+
 
     input:
     tuple val(meta), path(ref_depth_vcf), path(prep_dir)

From 6bf2d129a3a0f93285d6a406d4c2147e1661a12e Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 7 May 2025 09:21:59 +1000
Subject: [PATCH 26/88] remove gripss filtering subworkflow and modules

---
 conf/modules.config                    |  4 --
 subworkflows/local/gripss_filtering.nf | 90 --------------------------
 2 files changed, 94 deletions(-)
 delete mode 100644 subworkflows/local/gripss_filtering.nf

diff --git a/conf/modules.config b/conf/modules.config
index da15bd78..5b78059e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -98,10 +98,6 @@ process {
         ]
     }
 
-    withName: '.*:GRIPSS_FILTERING:(?:GERMLINE|SOMATIC)' {
-        ext.jarPath = '/opt/gripss/gripss.jar'
-    }
-
     withName: 'BOLT_SV_SOMATIC_ANNOTATE' {
         publishDir = [
             path: { "${params.outdir}" },
diff --git a/subworkflows/local/gripss_filtering.nf b/subworkflows/local/gripss_filtering.nf
deleted file mode 100644
index cb76a0c3..00000000
--- a/subworkflows/local/gripss_filtering.nf
+++ /dev/null
@@ -1,90 +0,0 @@
-//
-// GRIPSS performs SV filtering.
-//
-
-include { GRIPSS_GERMLINE as GERMLINE } from '../../modules/local/gripss/germline/main'
-include { GRIPSS_SOMATIC as SOMATIC   } from '../../modules/local/gripss/somatic/main'
-
-workflow GRIPSS_FILTERING {
-    take:
-        // Sample inputs
-        ch_inputs                // channel: [mandatory] [ meta ]
-        ch_gridss                // channel: [mandatory] [ meta, gridss_vcf ]
-
-        // Reference data
-        genome_fasta             // channel: [mandatory] /path/to/genome_fasta
-        genome_version           // channel: [mandatory] genome version
-        genome_fai               // channel: [mandatory] /path/to/genome_fai
-        breakend_pon             // channel: [mandatory] /path/to/breakend_pon
-        breakpoint_pon           // channel: [mandatory] /path/to/breakpoint_pon
-        known_fusions            // channel: [mandatory] /path/to/known_fusions
-        repeatmasker_annotations // channel: [mandatory] /path/to/repeatmasker_annotations
-
-    main:
-        // Channel for version.yml files
-        // channel: [ versions.yml ]
-        ch_versions = Channel.empty()
-
-        // Create process input channel
-        // channel: [ meta_gripss, gridss_vcf ]
-        ch_gripss_inputs = ch_gridss
-            .map { meta, gridss_vcf ->
-
-                def meta_gripss = [
-                    key: meta.id,
-                    id: meta.id,
-                    tumor_id: meta.tumor_id,
-                    normal_id: meta.normal_id,
-                ]
-
-                return [meta_gripss, gridss_vcf]
-            }
-
-        //
-        // MODULE: GRIPSS germline
-        //
-        GERMLINE(
-            ch_gripss_inputs,
-            genome_fasta,
-            genome_version,
-            genome_fai,
-            breakend_pon,
-            breakpoint_pon,
-            known_fusions,
-            repeatmasker_annotations,
-        )
-
-        ch_versions = ch_versions.mix(GERMLINE.out.versions)
-
-        //
-        // MODULE: GRIPSS somatic
-        //
-        SOMATIC(
-            ch_gripss_inputs,
-            genome_fasta,
-            genome_version,
-            genome_fai,
-            breakend_pon,
-            breakpoint_pon,
-            known_fusions,
-            repeatmasker_annotations,
-            [],
-        )
-
-        ch_versions = ch_versions.mix(SOMATIC.out.versions)
-
-        // Set outputs, restoring original meta
-        // channel: [ meta, gripss_vcf, gripss_tbi ]
-        ch_somatic_out = WorkflowSash.restoreMeta(SOMATIC.out.vcf, ch_inputs)
-        ch_somatic_unfiltered_out = WorkflowSash.restoreMeta(SOMATIC.out.vcf_unfiltered, ch_inputs)
-        ch_germline_out = WorkflowSash.restoreMeta(GERMLINE.out.vcf, ch_inputs)
-        ch_germline_unfiltered_out = WorkflowSash.restoreMeta(GERMLINE.out.vcf_unfiltered, ch_inputs)
-
-    emit:
-        somatic             = ch_somatic_out             // channel: [ meta, gripss_vcf, gripss_tbi ]
-        germline            = ch_germline_out            // channel: [ meta, gripss_vcf, gripss_tbi ]
-        somatic_unfiltered  = ch_somatic_unfiltered_out  // channel: [ meta, gripss_vcf, gripss_tbi ]
-        germline_unfiltered = ch_germline_unfiltered_out // channel: [ meta, gripss_vcf, gripss_tbi ]
-
-        versions = ch_versions                           // channel: [ versions.yml ]
-}

From 3996a977ef4e4eaa49e7091e64ad70eac503dd64 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 7 May 2025 13:51:44 +1000
Subject: [PATCH 27/88] change docker image cancer report

---
 modules/local/bolt/other/cancer_report/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index 4690eda8..847013e7 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/scwatts/bolt:0.2.13-gpgr'
+    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee'
 
     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)

From 81ebfe512192cb5fea4efa02dca5a0865f632e1b Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 7 May 2025 13:51:57 +1000
Subject: [PATCH 28/88] fix output path esvee

---
 conf/modules.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5b78059e..5f92b07a 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -171,7 +171,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/esvee/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/esvee/${filename}" }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/esvee/call/" }
         ]
     }
 
@@ -195,7 +195,7 @@ process {
         ]
     }
 
-  withName: '.*:LINX_PLOTTING:VISUALISER' {
+    withName: '.*:LINX_PLOTTING:VISUALISER' {
         ext.circosPath = '/opt/conda/bin/circos'
         publishDir = [
             path: { "${params.outdir}" },

From 3b9e0ab05e6f8742a1d1e96420fcc1dd1a876110 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 9 May 2025 11:31:29 +1000
Subject: [PATCH 29/88] fix output path esvee

---
 conf/modules.config | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5f92b07a..5a19d566 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -171,7 +171,10 @@ process {
         publishDir = [
             path: { "${params.outdir}/esvee/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/esvee/call/" }
+            saveAs: { fp ->
+                def fp_out = fp.replaceFirst(/caller\//, '')
+                return fp.equals('versions.yml') ? null : "${meta.key}/esvee/call/${fp_out}"
+            },
         ]
     }
 

From db8a53f658373fa6fca8a6f8909b510bfc935e61 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 9 May 2025 15:01:56 +1000
Subject: [PATCH 30/88] fix output path eSVee

---
 conf/modules.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5a19d566..d2696252 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -169,7 +169,7 @@ process {
 
     withName: 'ESVEE_CALL' {
         publishDir = [
-            path: { "${params.outdir}/esvee/" },
+            path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
             saveAs: { fp ->
                 def fp_out = fp.replaceFirst(/caller\//, '')

From b97feb565960507478572fdc6f48f64dc8626f58 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 9 May 2025 15:38:52 +1000
Subject: [PATCH 31/88] fix name output path esvee

---
 conf/modules.config                  | 5 +----
 subworkflows/local/purple_calling.nf | 6 +++---
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index d2696252..c8777ec1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -171,10 +171,7 @@ process {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
-            saveAs: { fp ->
-                def fp_out = fp.replaceFirst(/caller\//, '')
-                return fp.equals('versions.yml') ? null : "${meta.key}/esvee/call/${fp_out}"
-            },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/esvee/${filename}" }
         ]
     }
 
diff --git a/subworkflows/local/purple_calling.nf b/subworkflows/local/purple_calling.nf
index 6bd79424..1db09041 100644
--- a/subworkflows/local/purple_calling.nf
+++ b/subworkflows/local/purple_calling.nf
@@ -12,9 +12,9 @@ workflow PURPLE_CALLING {
         ch_cobalt                    // channel: [mandatory] [ meta, cobalt_dir ]
         ch_smlv_somatic              // channel: [optional]  [ meta, pave_vcf ]
         ch_smlv_germline             // channel: [optional]  [ meta, pave_vcf ]
-        ch_sv_somatic                // channel: [optional]  [ meta, gripss_vcf, gripss_tbi ]
-        ch_sv_germline               // channel: [optional]  [ meta, gripss_vcf, gripss_tbi ]
-        ch_sv_somatic_unfiltered     // channel: [optional]  [ meta, gripss_vcf, gripss_tbi ]
+        ch_sv_somatic                // channel: [optional]  [ meta, esvee_vcf, esvee_tbi ]
+        ch_sv_germline               // channel: [optional]  [ meta, esvee_vcf, esvee_tbi ]
+        ch_sv_somatic_unfiltered     // channel: [optional]  [ meta, esvee_vcf, esvee_tbi ]
 
         // Reference data
         genome_fasta                 // channel: [mandatory] /path/to/genome_fasta

From 9bd7ad2954de4df5127f7d128198cf62c0df304d Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 01:11:32 +0000
Subject: [PATCH 32/88] latest docker images

---
 modules/local/bolt/other/cancer_report/main.nf   | 2 +-
 modules/local/bolt/sv_somatic/prioritise/main.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index 847013e7..778ad080 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee'
+    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee-2'
 
     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)
diff --git a/modules/local/bolt/sv_somatic/prioritise/main.nf b/modules/local/bolt/sv_somatic/prioritise/main.nf
index 4ac07c7e..0a59abe6 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 'docker.io/qclayssen/bolt:oncoanalyser-v2'
+    container 'docker.io/qclayssen/bolt:oncoanalyser-v2-2'
 
     input:
     tuple val(meta), path(sv_vcf)

From 82a6d2e6a4cd19644db49e9112c889cffe13fceb Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 13:21:22 +1000
Subject: [PATCH 33/88] remove purple conda env, and deprecated input

---
 modules/local/esvee/call/environment.yml | 7 -------
 modules/local/purple/main.nf             | 3 +--
 2 files changed, 1 insertion(+), 9 deletions(-)
 delete mode 100644 modules/local/esvee/call/environment.yml

diff --git a/modules/local/esvee/call/environment.yml b/modules/local/esvee/call/environment.yml
deleted file mode 100644
index 01355c11..00000000
--- a/modules/local/esvee/call/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: esvee_call
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::hmftools-esvee=1.0.3
diff --git a/modules/local/purple/main.nf b/modules/local/purple/main.nf
index f267b00c..29512207 100644
--- a/modules/local/purple/main.nf
+++ b/modules/local/purple/main.nf
@@ -2,11 +2,10 @@ process PURPLE {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda "${moduleDir}/environment.yml"
     container 'docker.io/qclayssen/purple:4.1.0--1'
 
     input:
-    tuple val(meta), path(amber), path(cobalt), path(sv_tumor_vcf), path(sv_tumor_tbi), path(sv_tumor_unfiltered_vcf), path(sv_tumor_unfiltered_tbi), path(sv_normal_vcf), path(sv_normal_tbi), path(smlv_tumor_vcf), path(smlv_normal_vcf)
+    tuple val(meta), path(amber), path(cobalt), path(sv_tumor_vcf), path(sv_tumor_tbi), path(sv_normal_vcf), path(sv_normal_tbi), path(smlv_tumor_vcf), path(smlv_normal_vcf)
     path genome_fasta
     val genome_ver
     path genome_fai

From 7e9398e6d8d48935754fdaedfb1e6b6935420f14 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 13:21:42 +1000
Subject: [PATCH 34/88] tidy up

---
 workflows/sash.nf | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index fdafe4a6..ada5dc28 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -133,7 +133,7 @@ workflow SASH {
                 tumor_id: meta.tumor_id,
                 normal_id: meta.normal_id,
             ]
-            return [meta_bolt] + it[1..-1]
+            return [meta_bolt], *it[1..-1]
         }
 
     BOLT_SMLV_SOMATIC_RESCUE(
@@ -222,7 +222,6 @@ workflow SASH {
         ch_prep_dir,
     )
 
-    //TODO update ref data
     ESVEE_CALL(
         ch_call_inputs,
         genome.fasta,
@@ -235,7 +234,6 @@ workflow SASH {
 
     ch_esvee_somatic       = ESVEE_CALL.out.somatic_vcf
     ch_esvee_germline      = ESVEE_CALL.out.germline_vcf
-    ch_esvee_somatic_unfiltered = ESVEE_CALL.out.unfiltered_vcf
 
     //
     // CNV calling using UMCCR postprocessed variants
@@ -254,9 +252,8 @@ workflow SASH {
         //   * https://github.com/hartwigmedical/hmftools/blob/a2f82e5/purple/src/main/java/com/hartwig/hmftools/purple/germline/GermlineGenotypeEnrichment.java#L63
         //ch_smlv_germline_out,
         ch_smlv_germline_out.map { meta, vcf -> return [meta, []] },
-        ch_esvee_somatic,
-        ch_esvee_germline,
-        ch_esvee_somatic_unfiltered,
+        ESVEE_CALL.out.somatic_vcf,
+        ESVEE_CALL.out.germline_vcfe,
         genome.fasta,
         genome.version,
         genome.fai,
@@ -451,7 +448,7 @@ workflow SASH {
                 subject_id: meta.subject_id,
                 tumor_id: meta.tumor_id,
             ]
-            return [meta_bolt] + it[1..-1]
+            return [meta_bolt], *it[1..-1]
         }
 
     BOLT_OTHER_CANCER_REPORT(

From 03ca27ddd97875c5ec869b9a8e78e46814b8c62c Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 13:21:58 +1000
Subject: [PATCH 35/88] fix subworkflow deprecated input purple

---
 subworkflows/local/purple_calling.nf | 2 --
 1 file changed, 2 deletions(-)

diff --git a/subworkflows/local/purple_calling.nf b/subworkflows/local/purple_calling.nf
index 1db09041..ef73140c 100644
--- a/subworkflows/local/purple_calling.nf
+++ b/subworkflows/local/purple_calling.nf
@@ -14,7 +14,6 @@ workflow PURPLE_CALLING {
         ch_smlv_germline             // channel: [optional]  [ meta, pave_vcf ]
         ch_sv_somatic                // channel: [optional]  [ meta, esvee_vcf, esvee_tbi ]
         ch_sv_germline               // channel: [optional]  [ meta, esvee_vcf, esvee_tbi ]
-        ch_sv_somatic_unfiltered     // channel: [optional]  [ meta, esvee_vcf, esvee_tbi ]
 
         // Reference data
         genome_fasta                 // channel: [mandatory] /path/to/genome_fasta
@@ -41,7 +40,6 @@ workflow PURPLE_CALLING {
             ch_cobalt,
             // Optional inputs
             ch_sv_somatic,
-            ch_sv_somatic_unfiltered,
             ch_sv_germline,
             ch_smlv_somatic,
             ch_smlv_germline,

From 9f1528e1a41ef8e5c93b95944a0d878936df644d Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 13:27:35 +1000
Subject: [PATCH 36/88] linting

---
 workflows/sash.nf | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index ada5dc28..e9025eae 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -46,8 +46,8 @@ include { BOLT_SMLV_SOMATIC_REPORT   } from '../modules/local/bolt/smlv_somatic/
 include { BOLT_SMLV_SOMATIC_RESCUE   } from '../modules/local/bolt/smlv_somatic/rescue/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 { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
 include { ESVEE_CALL                 } from '../modules/local/esvee/call/main'
+include { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
 
 include { LINX_ANNOTATION            } from '../subworkflows/local/linx_annotation'
 include { LINX_PLOTTING              } from '../subworkflows/local/linx_plotting'
@@ -91,11 +91,11 @@ workflow SASH {
     ch_cobalt              = PREPARE_INPUT.out.cobalt
     ch_sage_somatic        = PREPARE_INPUT.out.sage_somatic
     ch_virusbreakend       = PREPARE_INPUT.out.virusbreakend
-    ch_input_hrd          = PREPARE_INPUT.out.hrd
+    ch_input_hrd           = PREPARE_INPUT.out.hrd
     ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline
     ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic
-    ch_ref_depth_vcf = PREPARE_INPUT.out.ref_depth_vcf
-    ch_prep_dir = PREPARE_INPUT.out.prep_dir
+    ch_ref_depth_vcf       = PREPARE_INPUT.out.ref_depth_vcf
+    ch_prep_dir            = PREPARE_INPUT.out.prep_dir
 
 
 
@@ -106,10 +106,10 @@ workflow SASH {
 
     // channel: [ meta ]
     PREPARE_REFERENCE()
-    genome = PREPARE_REFERENCE.out.genome
-    umccr_data = PREPARE_REFERENCE.out.umccr_data
-    hmf_data = PREPARE_REFERENCE.out.hmf_data
-    misc_data = PREPARE_REFERENCE.out.misc_data
+    genome               = PREPARE_REFERENCE.out.genome
+    umccr_data           = PREPARE_REFERENCE.out.umccr_data
+    hmf_data             = PREPARE_REFERENCE.out.hmf_data
+    misc_data            = PREPARE_REFERENCE.out.misc_data
 
 
 

From 754e7c3e83367bd4bcdf0ca5216bcf69aa593e5c Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 13:59:56 +1000
Subject: [PATCH 37/88] tidy up

---
 workflows/sash.nf | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index e9025eae..ae77b71b 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -209,14 +209,13 @@ workflow SASH {
     // channel: [ meta, smlv_germline_vcf ]
     ch_smlv_germline_out = WorkflowSash.restoreMeta(BOLT_SMLV_GERMLINE_PREPARE.out.vcf, ch_inputs)
 
+
+
+
     //
     // Somatic structural variants
 
     //
-    // MODULE: ESVEE call somatic structural variants
-    //
-    // Create process input channel
-    // channel: [meta_esvee, ref_depth_vcf, prep_dir]
     ch_call_inputs = WorkflowSash.groupByMeta(
         ch_ref_depth_vcf,
         ch_prep_dir,
@@ -232,9 +231,6 @@ workflow SASH {
         hmf_data.repeatmasker_annotations,
     )
 
-    ch_esvee_somatic       = ESVEE_CALL.out.somatic_vcf
-    ch_esvee_germline      = ESVEE_CALL.out.germline_vcf
-
     //
     // CNV calling using UMCCR postprocessed variants
     //

From aad37a72a60babf4bd2d933444c87c4afa0d6e7a Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 14:29:37 +1000
Subject: [PATCH 38/88] Uptade linx report for sash

---
 modules/local/linx/somatic/main.nf    |  2 --
 modules/local/linx/visualiser/main.nf | 24 ------------------------
 2 files changed, 26 deletions(-)

diff --git a/modules/local/linx/somatic/main.nf b/modules/local/linx/somatic/main.nf
index c6d7041d..e96e5d8e 100644
--- a/modules/local/linx/somatic/main.nf
+++ b/modules/local/linx/somatic/main.nf
@@ -12,7 +12,6 @@ process LINX_SOMATIC {
     path driver_gene_panel
     path gene_id_file
 
-
     output:
     tuple val(meta), path('linx_somatic/'), emit: annotation_dir
     path 'versions.yml'                   , emit: versions
@@ -24,7 +23,6 @@ process LINX_SOMATIC {
     def args = task.ext.args ?: ''
     def gene_id_file_arg = gene_id_file ? "-gene_id_file ${gene_id_file}" : ''
 
-
     def xmx_mod = task.ext.xmx_mod ?: 0.75
 
     """
diff --git a/modules/local/linx/visualiser/main.nf b/modules/local/linx/visualiser/main.nf
index a40646a3..02b17d98 100644
--- a/modules/local/linx/visualiser/main.nf
+++ b/modules/local/linx/visualiser/main.nf
@@ -54,30 +54,6 @@ process LINX_VISUALISER {
         -plot_out plots/all/ \\
         -data_out data/all/
 
-    # Rerun LINX to render only reportable cluster plots in a separate directory. While this is regenerating existing
-    # cluster plots, the number of reportable plots is generally very small and I prefer to rely on the internal LINX
-    # logic to determine whether a cluster is reportable rather than attempting to infer manually to copy out target
-    # plot files.
-
-    # The ORANGE report receives only reportable clusters while the gpgr LINX report receives chromosome and all cluster
-    # plots.
-
-    # https://github.com/hartwigmedical/hmftools/blob/linx-v1.24.1/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SampleData.java#L220-L236
-
-    linx \\
-        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
-        com.hartwig.hmftools.linx.visualiser.SvVisualiser \\
-        ${args2} \\
-        -sample ${meta.sample_id} \\
-        -vis_file_dir ${linx_annotation_dir} \\
-        -ref_genome_version ${genome_ver} \\
-        -ensembl_data_dir ${ensembl_data_resources} \\
-        -circos \$(which circos) \\
-        -plot_reportable \\
-        -threads ${task.cpus} \\
-        -plot_out plots/reportable/ \\
-        -data_out data/reportable/
-
     # Create placeholders to force FusionFS to create parent plot directory on S3
     if [[ \$(ls plots/ | wc -l) -eq 0 ]]; then
         touch plots/.keep;

From ee35c4ebfae23bce277f2af8fe5f19dc0a6dca9b Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 18:32:58 +1000
Subject: [PATCH 39/88] fix typo

---
 workflows/sash.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index ae77b71b..f8cc9779 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -133,7 +133,7 @@ workflow SASH {
                 tumor_id: meta.tumor_id,
                 normal_id: meta.normal_id,
             ]
-            return [meta_bolt], *it[1..-1]
+            return [meta_bolt], *it[1..-1]]
         }
 
     BOLT_SMLV_SOMATIC_RESCUE(
@@ -444,7 +444,7 @@ workflow SASH {
                 subject_id: meta.subject_id,
                 tumor_id: meta.tumor_id,
             ]
-            return [meta_bolt], *it[1..-1]
+            return [meta_bolt], *it[1..-1]]
         }
 
     BOLT_OTHER_CANCER_REPORT(

From 80081b143acca629e420638c0c481067a0dca53a Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 18:37:14 +1000
Subject: [PATCH 40/88] same typo

---
 workflows/sash.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index f8cc9779..9ff3c89f 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -133,7 +133,7 @@ workflow SASH {
                 tumor_id: meta.tumor_id,
                 normal_id: meta.normal_id,
             ]
-            return [meta_bolt], *it[1..-1]]
+            return [[meta_bolt], *it[1..-1]]
         }
 
     BOLT_SMLV_SOMATIC_RESCUE(
@@ -444,7 +444,7 @@ workflow SASH {
                 subject_id: meta.subject_id,
                 tumor_id: meta.tumor_id,
             ]
-            return [meta_bolt], *it[1..-1]]
+            return [[meta_bolt], *it[1..-1]]
         }
 
     BOLT_OTHER_CANCER_REPORT(

From 3a0cae80801373807ec29a202d27b3ef33d8b27c Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 12 May 2025 18:38:59 +1000
Subject: [PATCH 41/88] still ...

---
 workflows/sash.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 9ff3c89f..4da00a7d 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -133,7 +133,7 @@ workflow SASH {
                 tumor_id: meta.tumor_id,
                 normal_id: meta.normal_id,
             ]
-            return [[meta_bolt], *it[1..-1]]
+            return [meta_bolt, *it[1..-1]]
         }
 
     BOLT_SMLV_SOMATIC_RESCUE(
@@ -444,7 +444,7 @@ workflow SASH {
                 subject_id: meta.subject_id,
                 tumor_id: meta.tumor_id,
             ]
-            return [[meta_bolt], *it[1..-1]]
+            return [meta_bolt, *it[1..-1]]
         }
 
     BOLT_OTHER_CANCER_REPORT(

From 78d9e3c6198fc203cac4ba7ec2b592bd45b0f05a Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 09:55:31 +1000
Subject: [PATCH 42/88] typo

---
 workflows/sash.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 4da00a7d..ac34d065 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -249,7 +249,7 @@ workflow SASH {
         //ch_smlv_germline_out,
         ch_smlv_germline_out.map { meta, vcf -> return [meta, []] },
         ESVEE_CALL.out.somatic_vcf,
-        ESVEE_CALL.out.germline_vcfe,
+        ESVEE_CALL.out.germline_vcf,
         genome.fasta,
         genome.version,
         genome.fai,

From 1bf7155957922fdd1f3c5cce166aaa2e9a705f73 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 11:55:30 +1000
Subject: [PATCH 43/88] touch file for pcgr stub run

---
 modules/local/bolt/smlv_somatic/report/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/local/bolt/smlv_somatic/report/main.nf b/modules/local/bolt/smlv_somatic/report/main.nf
index e293cd4c..c5bbf6b9 100644
--- a/modules/local/bolt/smlv_somatic/report/main.nf
+++ b/modules/local/bolt/smlv_somatic/report/main.nf
@@ -60,6 +60,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
     stub:
     """
     mkdir -p output/pcgr/
+    touch output/pcgr/pcgr.stub
     touch output/af_tumor.txt
     touch output/af_tumor_keygenes.txt
     touch output/${meta.tumor_id}.somatic.variant_counts_type.yaml

From f5852b0882489f30ef4f150b9be821702dfe50b7 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 13:33:06 +1000
Subject: [PATCH 44/88] touch stub file multiqc

---
 modules/local/bolt/other/multiqc_report/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/local/bolt/other/multiqc_report/main.nf b/modules/local/bolt/other/multiqc_report/main.nf
index 5dfb9b11..1f2b3305 100644
--- a/modules/local/bolt/other/multiqc_report/main.nf
+++ b/modules/local/bolt/other/multiqc_report/main.nf
@@ -35,6 +35,7 @@ process BOLT_OTHER_MULTIQC_REPORT {
     stub:
     """
     mkdir -p multiqc_report/multiqc_data/
+    touch multiqc_report/multiqc.stub
     touch ${meta.tumor_id}.multiqc.html
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """

From 2497ce5c667b88794ad9428ac279ccd9e38f3a59 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 14:07:56 +1000
Subject: [PATCH 45/88] tidy up

---
 modules/local/bolt/other/multiqc_report/main.nf | 2 +-
 modules/local/linx/visualiser/main.nf           | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/local/bolt/other/multiqc_report/main.nf b/modules/local/bolt/other/multiqc_report/main.nf
index 1f2b3305..d35be097 100644
--- a/modules/local/bolt/other/multiqc_report/main.nf
+++ b/modules/local/bolt/other/multiqc_report/main.nf
@@ -35,7 +35,7 @@ process BOLT_OTHER_MULTIQC_REPORT {
     stub:
     """
     mkdir -p multiqc_report/multiqc_data/
-    touch multiqc_report/multiqc.stub
+    touch multiqc_report/multiqc_data/multiqc.stub
     touch ${meta.tumor_id}.multiqc.html
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
diff --git a/modules/local/linx/visualiser/main.nf b/modules/local/linx/visualiser/main.nf
index 02b17d98..8eb1ae96 100644
--- a/modules/local/linx/visualiser/main.nf
+++ b/modules/local/linx/visualiser/main.nf
@@ -18,7 +18,6 @@ process LINX_VISUALISER {
 
     script:
     def args = task.ext.args ?: ''
-    def args2 = task.ext.args2 ?: ''
 
     def xmx_mod = task.ext.xmx_mod ?: 0.75
 

From d977f2bb4c7a08ff14e34183b481df2aa50a773f Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 14:13:14 +1000
Subject: [PATCH 46/88] test fix out put file eSVee

---
 workflows/sash.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index ac34d065..c02d7779 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -216,11 +216,11 @@ workflow SASH {
     // Somatic structural variants
 
     //
-    ch_call_inputs = WorkflowSash.groupByMeta(
+    call_inputs = WorkflowSash.groupByMeta(
         ch_ref_depth_vcf,
         ch_prep_dir,
     )
-
+    ch_call_inputs = WorkflowSash.restoreMeta(call_inputs, ch_inputs)
     ESVEE_CALL(
         ch_call_inputs,
         genome.fasta,

From 29c0f62e1cbaa3b1b35c9e259d9ecf6adf922a31 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 14:36:28 +1000
Subject: [PATCH 47/88] add more stubs

---
 modules/local/bolt/other/cancer_report/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index 778ad080..b2c3194d 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -60,6 +60,7 @@ process BOLT_OTHER_CANCER_REPORT {
     stub:
     """
     mkdir -p output/
+    mkdir -p output/cancer_report.stub
     touch ${meta.tumor_id}.cancer_report.html
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """

From 8b837b5427276529d221fba89e2e88ca9fdea4c7 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 14:50:10 +1000
Subject: [PATCH 48/88] test fix ouput path esvee

---
 conf/modules.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index c8777ec1..32a24956 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -167,11 +167,11 @@ process {
         ]
     }
 
-    withName: 'ESVEE_CALL' {
+    withName: '.*:ESVEE_CALL' {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/esvee/${filename}" }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/esvee/${filename}" }
         ]
     }
 

From 9611cc68a021535ec7d4b052226b23b82274ab64 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 15:03:47 +1000
Subject: [PATCH 49/88] fix stub ...

---
 modules/local/bolt/other/cancer_report/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index b2c3194d..feb542be 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -60,7 +60,7 @@ process BOLT_OTHER_CANCER_REPORT {
     stub:
     """
     mkdir -p output/
-    mkdir -p output/cancer_report.stub
+    touch -p output/cancer_report.stub
     touch ${meta.tumor_id}.cancer_report.html
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """

From f0325e9d5872050431fd9ade11d4f47c365740d0 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 15:14:55 +1000
Subject: [PATCH 50/88] fix typo

---
 conf/modules.config                            | 2 +-
 modules/local/bolt/other/cancer_report/main.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 32a24956..c67f481e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -167,7 +167,7 @@ process {
         ]
     }
 
-    withName: '.*:ESVEE_CALL' {
+    withName: 'ESVEE_CALL' {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index feb542be..ab41d0bf 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -60,7 +60,7 @@ process BOLT_OTHER_CANCER_REPORT {
     stub:
     """
     mkdir -p output/
-    touch -p output/cancer_report.stub
+    touch output/cancer_report.stub
     touch ${meta.tumor_id}.cancer_report.html
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """

From 2a096878bd30ab68ccb7e7c72655d7013c92ecbc Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 15:16:39 +1000
Subject: [PATCH 51/88] fix channel

---
 workflows/sash.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index c02d7779..16d20b54 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -216,11 +216,11 @@ workflow SASH {
     // Somatic structural variants
 
     //
-    call_inputs = WorkflowSash.groupByMeta(
+    ch_call_inputs = WorkflowSash.groupByMeta(
         ch_ref_depth_vcf,
-        ch_prep_dir,
+        ch_prep_dir
     )
-    ch_call_inputs = WorkflowSash.restoreMeta(call_inputs, ch_inputs)
+
     ESVEE_CALL(
         ch_call_inputs,
         genome.fasta,

From 210c5ca1cdb0efa43a0fbf29e89ff71496d4eb4b Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 15:36:13 +1000
Subject: [PATCH 52/88] change in prepare input and add doc

---
 conf/modules.config                 |  1 +
 subworkflows/local/prepare_input.nf | 42 +++++++++++++++++------------
 workflows/sash.nf                   | 27 ++++++++++---------
 3 files changed, 41 insertions(+), 29 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index c67f481e..821bf08b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -171,6 +171,7 @@ process {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
+            // Use meta.id as it's always defined, unlike meta.key which was causing null issues
             saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/esvee/${filename}" }
         ]
     }
diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index d9cdbc6d..6ea4bcaa 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -45,19 +45,17 @@ workflow PREPARE_INPUT {
             def base = file(meta.oncoanalyser_dir).toUriString()
             return [meta, "${base}/amber/"]
         }
+
         def ch_cobalt = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             return [meta, "${base}/cobalt/"]
         }
-        def ch_ref_depth_vcf = ch_metas.map { meta ->
-            def base = file(meta.oncoanalyser_dir).toUriString()
-            def vcf = "${base}/esvee/depth_annotation/${meta.tumor_id}.esvee.ref_depth.vcf.gz"
-            return [meta, vcf]
-        }
-        def ch_prep_dir = ch_metas.map { meta ->
+
+        def ch_call_inputs = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def dir = "${base}/esvee/prep/"
-            return [meta, dir]
+            def vcf = "${base}/esvee/depth_annotation/${meta.tumor_id}.esvee.ref_depth.vcf.gz"
+            return [meta, dir, vcf]
         }
 
         def ch_sage_somatic = ch_metas.map { meta ->
@@ -65,32 +63,42 @@ workflow PREPARE_INPUT {
             def vcf = "${base}/sage/somatic/${meta.tumor_id}.sage.somatic.vcf.gz"
             return [meta, vcf, "${vcf}.tbi"]
         }
+
         def ch_virusbreakend = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             return [meta, "${base}/virusbreakend/"]
         }
+
         def ch_input_hrd = ch_metas.map { meta ->
             def base = file(meta.dragen_somatic_dir).toUriString()
             return [meta, "${base}/${meta.tumor_id}.hrdscore.csv"]
         }
+
         def ch_input_vcf_germline = ch_metas.map { meta ->
             def base = file(meta.dragen_germline_dir).toUriString()
             return [meta, "${base}/${meta.normal_id}.hard-filtered.vcf.gz"]
         }
+
         def ch_input_vcf_somatic = ch_metas.map { meta ->
             def base = file(meta.dragen_somatic_dir).toUriString()
             def vcf = "${base}/${meta.tumor_id}.hard-filtered.vcf.gz"
             return [meta, vcf, "${vcf}.tbi"]
         }
     emit:
-        metas = ch_metas
-        amber = ch_amber
-        cobalt = ch_cobalt
-        sage_somatic = ch_sage_somatic
-        virusbreakend = ch_virusbreakend
-        hrd = ch_input_hrd
-        vcf_germline = ch_input_vcf_germline
-        vcf_somatic = ch_input_vcf_somatic
-        ref_depth_vcf = ch_ref_depth_vcf
-        prep_dir = ch_prep_dir
+        // Meta information for each sample
+        metas = ch_metas                   // channel: [ meta ]
+
+        // Oncoanalyser inputs
+        amber = ch_amber                   // channel: [ meta, amber_dir ]
+        cobalt = ch_cobalt                 // channel: [ meta, cobalt_dir ]
+        sage_somatic = ch_sage_somatic     // channel: [ meta, vcf, tbi ]
+        virusbreakend = ch_virusbreakend   // channel: [ meta, virusbreakend_dir ]
+
+        // DRAGEN inputs
+        hrd = ch_input_hrd                 // channel: [ meta, hrdscore_csv ]
+        vcf_germline = ch_input_vcf_germline // channel: [ meta, germline_vcf ]
+        vcf_somatic = ch_input_vcf_somatic   // channel: [ meta, somatic_vcf, tbi ]
+
+        // eSVee inputs
+        call_inputs = ch_call_inputs             // channel: [ meta, esvee_prep_dir, esvee_ref_depth_vcf ]
 }
diff --git a/workflows/sash.nf b/workflows/sash.nf
index 16d20b54..0ec538d8 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -81,21 +81,24 @@ workflow SASH {
     // Prepare inputs from samplesheet
     //
 
-    // channel: [ meta ]
     PREPARE_INPUT(
         file(params.input),
     )
-    ch_inputs = PREPARE_INPUT.out.metas
-
-    ch_amber               = PREPARE_INPUT.out.amber
-    ch_cobalt              = PREPARE_INPUT.out.cobalt
-    ch_sage_somatic        = PREPARE_INPUT.out.sage_somatic
-    ch_virusbreakend       = PREPARE_INPUT.out.virusbreakend
-    ch_input_hrd           = PREPARE_INPUT.out.hrd
-    ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline
-    ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic
-    ch_ref_depth_vcf       = PREPARE_INPUT.out.ref_depth_vcf
-    ch_prep_dir            = PREPARE_INPUT.out.prep_dir
+    ch_inputs = PREPARE_INPUT.out.metas            // channel: [ meta ]
+
+    // OncoAnalyser outputs
+    ch_amber               = PREPARE_INPUT.out.amber             // channel: [ meta, amber_dir ]
+    ch_cobalt              = PREPARE_INPUT.out.cobalt            // channel: [ meta, cobalt_dir ]
+    ch_sage_somatic        = PREPARE_INPUT.out.sage_somatic      // channel: [ meta, vcf, tbi ]
+    ch_virusbreakend       = PREPARE_INPUT.out.virusbreakend     // channel: [ meta, virusbreakend_dir ]
+
+    // DRAGEN outputs
+    ch_input_hrd           = PREPARE_INPUT.out.hrd               // channel: [ meta, hrdscore_csv ]
+    ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline      // channel: [ meta, germline_vcf ]
+    ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic       // channel: [ meta, somatic_vcf, tbi ]
+
+    // eSVee inputs
+    ch_call_inputs         = PREPARE_INPUT.out.call_inputs       // channel: [ meta, esvee_prep_dir, esvee_ref_depth_vcf ]
 
 
 

From 22ca727cdf1b663e60d5bd2ef38aec5cb0061a2e Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 16:05:21 +1000
Subject: [PATCH 53/88] linting and version esvee

---
 workflows/sash.nf | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 0ec538d8..083ea6ef 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -234,6 +234,7 @@ workflow SASH {
         hmf_data.repeatmasker_annotations,
     )
 
+    ch_versions = ch_versions.mix(ESVEE_CALL.out.versions)
     //
     // CNV calling using UMCCR postprocessed variants
     //
@@ -251,6 +252,7 @@ workflow SASH {
         //   * https://github.com/hartwigmedical/hmftools/blob/a2f82e5/purple/src/main/java/com/hartwig/hmftools/purple/germline/GermlineGenotypeEnrichment.java#L63
         //ch_smlv_germline_out,
         ch_smlv_germline_out.map { meta, vcf -> return [meta, []] },
+
         ESVEE_CALL.out.somatic_vcf,
         ESVEE_CALL.out.germline_vcf,
         genome.fasta,
@@ -265,6 +267,9 @@ workflow SASH {
         hmf_data.purple_germline_del,
     )
 
+
+
+
     //
     // Small variant reporting (PCGR, CPSR, stats)
     //

From fd1e84f4255e3b55c6dfb7db492518714fe1c4a3 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 17:53:33 +1000
Subject: [PATCH 54/88] fix deprecated channel

---
 workflows/sash.nf | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 083ea6ef..4a1c0507 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -219,10 +219,6 @@ workflow SASH {
     // Somatic structural variants
 
     //
-    ch_call_inputs = WorkflowSash.groupByMeta(
-        ch_ref_depth_vcf,
-        ch_prep_dir
-    )
 
     ESVEE_CALL(
         ch_call_inputs,

From 73fcdc20dd5e9c7bc1d1b36a03e9bb7e2f049e54 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 17:57:58 +1000
Subject: [PATCH 55/88] uniform doc

---
 workflows/sash.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 4a1c0507..753b560c 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -86,13 +86,13 @@ workflow SASH {
     )
     ch_inputs = PREPARE_INPUT.out.metas            // channel: [ meta ]
 
-    // OncoAnalyser outputs
+    // OncoAnalyser inputs
     ch_amber               = PREPARE_INPUT.out.amber             // channel: [ meta, amber_dir ]
     ch_cobalt              = PREPARE_INPUT.out.cobalt            // channel: [ meta, cobalt_dir ]
     ch_sage_somatic        = PREPARE_INPUT.out.sage_somatic      // channel: [ meta, vcf, tbi ]
     ch_virusbreakend       = PREPARE_INPUT.out.virusbreakend     // channel: [ meta, virusbreakend_dir ]
 
-    // DRAGEN outputs
+    // DRAGEN inputs
     ch_input_hrd           = PREPARE_INPUT.out.hrd               // channel: [ meta, hrdscore_csv ]
     ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline      // channel: [ meta, germline_vcf ]
     ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic       // channel: [ meta, somatic_vcf, tbi ]

From 83b15a728995e51a9972106732ffe4182a139650 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 13 May 2025 18:14:03 +1000
Subject: [PATCH 56/88] fix order esvee channel

---
 subworkflows/local/prepare_input.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 6ea4bcaa..a7f6e2b3 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -53,9 +53,9 @@ workflow PREPARE_INPUT {
 
         def ch_call_inputs = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
-            def dir = "${base}/esvee/prep/"
             def vcf = "${base}/esvee/depth_annotation/${meta.tumor_id}.esvee.ref_depth.vcf.gz"
-            return [meta, dir, vcf]
+            def dir = "${base}/esvee/prep/"
+            return [meta, vcf, dir]
         }
 
         def ch_sage_somatic = ch_metas.map { meta ->

From 8b7f806a16bd795f1041c46c909e3372b102b77e Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 14 May 2025 14:11:13 +1000
Subject: [PATCH 57/88] add stup block

---
 modules/nf-core/custom/dumpsoftwareversions/main.nf | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 800a6099..87adf06a 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -21,4 +21,11 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     script:
     def args = task.ext.args ?: ''
     template 'dumpsoftwareversions.py'
+
+    stub:
+    """
+    touch software_versions.yml
+    touch software_versions_mqc.yml
+    touch versions.yml
+    """
 }

From ab31d5d58489885ee667b9e5c36eb27b39637bf0 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 14 May 2025 14:27:03 +1000
Subject: [PATCH 58/88] change esvee meta to use key tag

---
 conf/modules.config                 | 3 +--
 subworkflows/local/prepare_input.nf | 9 ++++++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 821bf08b..c8777ec1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -171,8 +171,7 @@ process {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
-            // Use meta.id as it's always defined, unlike meta.key which was causing null issues
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/esvee/${filename}" }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/esvee/${filename}" }
         ]
     }
 
diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index a7f6e2b3..d1040ed5 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -52,10 +52,17 @@ workflow PREPARE_INPUT {
         }
 
         def ch_call_inputs = ch_metas.map { meta ->
+            def meta_esvee = [
+                key: meta.id,
+                id: meta.id,
+                tumor_id: meta.tumor_id,
+                normal_id: meta.normal_id,
+            ]
+
             def base = file(meta.oncoanalyser_dir).toUriString()
             def vcf = "${base}/esvee/depth_annotation/${meta.tumor_id}.esvee.ref_depth.vcf.gz"
             def dir = "${base}/esvee/prep/"
-            return [meta, vcf, dir]
+            return [meta_esvee, vcf, dir]
         }
 
         def ch_sage_somatic = ch_metas.map { meta ->

From 6db7b5d9482c5cbd5086794571fdb3092df70e9b Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 14 May 2025 16:22:59 +1000
Subject: [PATCH 59/88] clean up

---
 modules/local/linx/germline/environment.yml         |  7 -------
 modules/local/linx/somatic/environment.yml          |  7 -------
 modules/local/linx/visualiser/environment.yml       |  7 -------
 modules/local/linxreport/environment.yml            |  7 -------
 modules/local/purple/environment.yml                |  7 -------
 modules/nf-core/custom/dumpsoftwareversions/main.nf |  2 +-
 subworkflows/local/prepare_input.nf                 |  6 +++---
 workflows/sash.nf                                   | 11 ++++++++---
 8 files changed, 12 insertions(+), 42 deletions(-)
 delete mode 100644 modules/local/linx/germline/environment.yml
 delete mode 100644 modules/local/linx/somatic/environment.yml
 delete mode 100644 modules/local/linx/visualiser/environment.yml
 delete mode 100644 modules/local/linxreport/environment.yml
 delete mode 100644 modules/local/purple/environment.yml

diff --git a/modules/local/linx/germline/environment.yml b/modules/local/linx/germline/environment.yml
deleted file mode 100644
index 57471f2c..00000000
--- a/modules/local/linx/germline/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: linx_germline
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::hmftools-linx=2.0
diff --git a/modules/local/linx/somatic/environment.yml b/modules/local/linx/somatic/environment.yml
deleted file mode 100644
index 4d244fae..00000000
--- a/modules/local/linx/somatic/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: linx_somatic
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::hmftools-linx=2.0
diff --git a/modules/local/linx/visualiser/environment.yml b/modules/local/linx/visualiser/environment.yml
deleted file mode 100644
index 5dadb70e..00000000
--- a/modules/local/linx/visualiser/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: linx_visualiser
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::hmftools-linx=2.0
diff --git a/modules/local/linxreport/environment.yml b/modules/local/linxreport/environment.yml
deleted file mode 100644
index 71113340..00000000
--- a/modules/local/linxreport/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: linxreport
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::r-linxreport=1.1.0
diff --git a/modules/local/purple/environment.yml b/modules/local/purple/environment.yml
deleted file mode 100644
index fb18f1e6..00000000
--- a/modules/local/purple/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: purple
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::hmftools-purple=4.1
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 87adf06a..f3b3d8a8 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -26,6 +26,6 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     """
     touch software_versions.yml
     touch software_versions_mqc.yml
-    touch versions.yml
+    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """
 }
diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index d1040ed5..49ccf207 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -98,13 +98,13 @@ workflow PREPARE_INPUT {
         // Oncoanalyser inputs
         amber = ch_amber                   // channel: [ meta, amber_dir ]
         cobalt = ch_cobalt                 // channel: [ meta, cobalt_dir ]
-        sage_somatic = ch_sage_somatic     // channel: [ meta, vcf, tbi ]
+        sage_somatic = ch_sage_somatic     // channel: [ meta, sage_somatic_vcf, sage_somatic_tbi ]
         virusbreakend = ch_virusbreakend   // channel: [ meta, virusbreakend_dir ]
 
         // DRAGEN inputs
         hrd = ch_input_hrd                 // channel: [ meta, hrdscore_csv ]
-        vcf_germline = ch_input_vcf_germline // channel: [ meta, germline_vcf ]
-        vcf_somatic = ch_input_vcf_somatic   // channel: [ meta, somatic_vcf, tbi ]
+        vcf_germline = ch_input_vcf_germline // channel: [ meta, dragen_germline_vcf ]
+        vcf_somatic = ch_input_vcf_somatic   // channel: [ meta, dragen_somatic_vcf, dragen_somatic_tbi ]
 
         // eSVee inputs
         call_inputs = ch_call_inputs             // channel: [ meta, esvee_prep_dir, esvee_ref_depth_vcf ]
diff --git a/workflows/sash.nf b/workflows/sash.nf
index 753b560c..1ce4d20b 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -89,13 +89,13 @@ workflow SASH {
     // OncoAnalyser inputs
     ch_amber               = PREPARE_INPUT.out.amber             // channel: [ meta, amber_dir ]
     ch_cobalt              = PREPARE_INPUT.out.cobalt            // channel: [ meta, cobalt_dir ]
-    ch_sage_somatic        = PREPARE_INPUT.out.sage_somatic      // channel: [ meta, vcf, tbi ]
+    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 ]
 
     // DRAGEN inputs
     ch_input_hrd           = PREPARE_INPUT.out.hrd               // channel: [ meta, hrdscore_csv ]
-    ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline      // channel: [ meta, germline_vcf ]
-    ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic       // channel: [ meta, somatic_vcf, tbi ]
+    ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline      // channel: [ meta, dragen_germline_vcf ]
+    ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic       // channel: [ meta, dragen_somatic_vcf, dragen_somatic_tbi ]
 
     // eSVee inputs
     ch_call_inputs         = PREPARE_INPUT.out.call_inputs       // channel: [ meta, esvee_prep_dir, esvee_ref_depth_vcf ]
@@ -190,6 +190,7 @@ workflow SASH {
     // Germline small variants
     //
 
+    // channel: [ meta_bolt, dragen_germline_vcf ]
     ch_smlv_germline_prepare_inputs = ch_input_vcf_germline
         .map { meta, dragen_vcf ->
 
@@ -231,6 +232,10 @@ workflow SASH {
     )
 
     ch_versions = ch_versions.mix(ESVEE_CALL.out.versions)
+
+
+
+
     //
     // CNV calling using UMCCR postprocessed variants
     //

From 0f1748796770ce4c461211910b63b4449c4292ff Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 15 May 2025 11:39:16 +1000
Subject: [PATCH 60/88] add utils_nfcore_pipeline

---
 modules.json                                  |   9 +
 modules/nf-core/fastqc/main.nf                |  51 +++
 modules/nf-core/fastqc/meta.yml               |  52 +++
 modules/nf-core/multiqc/main.nf               |  53 +++
 modules/nf-core/multiqc/meta.yml              |  56 +++
 .../nf-core/utils_nfcore_pipeline/main.nf     | 419 ++++++++++++++++++
 .../nf-core/utils_nfcore_pipeline/meta.yml    |  24 +
 .../tests/main.function.nf.test               | 126 ++++++
 .../tests/main.function.nf.test.snap          | 136 ++++++
 .../tests/main.workflow.nf.test               |  29 ++
 .../tests/main.workflow.nf.test.snap          |  19 +
 .../tests/nextflow.config                     |   9 +
 12 files changed, 983 insertions(+)
 create mode 100644 modules/nf-core/fastqc/main.nf
 create mode 100644 modules/nf-core/fastqc/meta.yml
 create mode 100644 modules/nf-core/multiqc/main.nf
 create mode 100644 modules/nf-core/multiqc/meta.yml
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
 create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config

diff --git a/modules.json b/modules.json
index f5341730..42c1b398 100644
--- a/modules.json
+++ b/modules.json
@@ -21,6 +21,15 @@
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "utils_nfcore_pipeline": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         }
     }
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
new file mode 100644
index 00000000..9ae58381
--- /dev/null
+++ b/modules/nf-core/fastqc/main.nf
@@ -0,0 +1,51 @@
+process FASTQC {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "bioconda::fastqc=0.11.9"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
+        'quay.io/biocontainers/fastqc:0.11.9--0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.zip") , emit: zip
+    path  "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Make list of old name and new name pairs to use for renaming in the bash while loop
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    """
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+    fastqc $args --threads $task.cpus $renamed_files
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+    touch ${prefix}.zip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
new file mode 100644
index 00000000..4da5bb5a
--- /dev/null
+++ b/modules/nf-core/fastqc/meta.yml
@@ -0,0 +1,52 @@
+name: fastqc
+description: Run FastQC on sequenced reads
+keywords:
+  - quality control
+  - qc
+  - adapters
+  - fastq
+tools:
+  - fastqc:
+      description: |
+        FastQC gives general quality metrics about your reads.
+        It provides information about the quality score distribution
+        across your reads, the per base sequence content (%A/C/G/T).
+        You get information about adapter contamination and other
+        overrepresented sequences.
+      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+      licence: ["GPL-2.0-only"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - html:
+      type: file
+      description: FastQC report
+      pattern: "*_{fastqc.html}"
+  - zip:
+      type: file
+      description: FastQC report archive
+      pattern: "*_{fastqc.zip}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@grst"
+  - "@ewels"
+  - "@FelixKrueger"
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
new file mode 100644
index 00000000..4b604749
--- /dev/null
+++ b/modules/nf-core/multiqc/main.nf
@@ -0,0 +1,53 @@
+process MULTIQC {
+    label 'process_single'
+
+    conda "bioconda::multiqc=1.14"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+
+    input:
+    path  multiqc_files, stageAs: "?/*"
+    path(multiqc_config)
+    path(extra_multiqc_config)
+    path(multiqc_logo)
+
+    output:
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "versions.yml"        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def config = multiqc_config ? "--config $multiqc_config" : ''
+    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    """
+    multiqc \\
+        --force \\
+        $args \\
+        $config \\
+        $extra_config \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
new file mode 100644
index 00000000..f93b5ee5
--- /dev/null
+++ b/modules/nf-core/multiqc/meta.yml
@@ -0,0 +1,56 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: MultiQC
+description: Aggregate results from bioinformatics analyses across many samples into a single report
+keywords:
+  - QC
+  - bioinformatics tools
+  - Beautiful stand-alone HTML report
+tools:
+  - multiqc:
+      description: |
+        MultiQC searches a given directory for analysis logs and compiles a HTML report.
+        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+      homepage: https://multiqc.info/
+      documentation: https://multiqc.info/docs/
+      licence: ["GPL-3.0-or-later"]
+
+input:
+  - multiqc_files:
+      type: file
+      description: |
+        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+
+output:
+  - report:
+      type: file
+      description: MultiQC report file
+      pattern: "multiqc_report.html"
+  - data:
+      type: directory
+      description: MultiQC data dir
+      pattern: "multiqc_data"
+  - plots:
+      type: file
+      description: Plots created by MultiQC
+      pattern: "*_data"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"
+  - "@jfy133"
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
new file mode 100644
index 00000000..bfd25876
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -0,0 +1,419 @@
+//
+// Subworkflow with utility functions specific to the nf-core pipeline template
+//
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    SUBWORKFLOW DEFINITION
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow UTILS_NFCORE_PIPELINE {
+    take:
+    nextflow_cli_args
+
+    main:
+    valid_config = checkConfigProvided()
+    checkProfileProvided(nextflow_cli_args)
+
+    emit:
+    valid_config
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    FUNCTIONS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+//
+//  Warn if a -profile or Nextflow config has not been provided to run the pipeline
+//
+def checkConfigProvided() {
+    def valid_config = true as Boolean
+    if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
+        log.warn(
+            "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + "   (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + "   (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + "   (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n "
+        )
+        valid_config = false
+    }
+    return valid_config
+}
+
+//
+// Exit pipeline if --profile contains spaces
+//
+def checkProfileProvided(nextflow_cli_args) {
+    if (workflow.profile.endsWith(',')) {
+        error(
+            "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
+    }
+    if (nextflow_cli_args[0]) {
+        log.warn(
+            "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n"
+        )
+    }
+}
+
+//
+// Generate workflow version string
+//
+def getWorkflowVersion() {
+    def version_string = "" as String
+    if (workflow.manifest.version) {
+        def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
+        version_string += "${prefix_v}${workflow.manifest.version}"
+    }
+
+    if (workflow.commitId) {
+        def git_shortsha = workflow.commitId.substring(0, 7)
+        version_string += "-g${git_shortsha}"
+    }
+
+    return version_string
+}
+
+//
+// Get software versions for pipeline
+//
+def processVersionsFromYAML(yaml_file) {
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] }
+    return yaml.dumpAsMap(versions).trim()
+}
+
+//
+// Get workflow version for pipeline
+//
+def workflowVersionToYAML() {
+    return """
+    Workflow:
+        ${workflow.manifest.name}: ${getWorkflowVersion()}
+        Nextflow: ${workflow.nextflow.version}
+    """.stripIndent().trim()
+}
+
+//
+// Get channel of software versions used in pipeline in YAML format
+//
+def softwareVersionsToYAML(ch_versions) {
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
+}
+
+//
+// Get workflow summary for MultiQC
+//
+def paramsSummaryMultiqc(summary_params) {
+    def summary_section = ''
+    summary_params
+        .keySet()
+        .each { group ->
+            def group_params = summary_params.get(group)
+            // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>${group}</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                group_params
+                    .keySet()
+                    .sort()
+                    .each { param ->
+                        summary_section += "        <dt>${param}</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                    }
+                summary_section += "    </dl>\n"
+            }
+        }
+
+    def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String
+    yaml_file_text     += "description: ' - this information is collected when the pipeline is started.'\n"
+    yaml_file_text     += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+    yaml_file_text     += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+    yaml_file_text     += "plot_type: 'html'\n"
+    yaml_file_text     += "data: |\n"
+    yaml_file_text     += "${summary_section}"
+
+    return yaml_file_text
+}
+
+//
+// ANSII colours used for terminal logging
+//
+def logColours(monochrome_logs=true) {
+    def colorcodes = [:] as Map
+
+    // Reset / Meta
+    colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+    colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+    colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+    colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+    colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+    colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+    colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
+
+    // Regular Colors
+    colorcodes['black']  = monochrome_logs ? '' : "\033[0;30m"
+    colorcodes['red']    = monochrome_logs ? '' : "\033[0;31m"
+    colorcodes['green']  = monochrome_logs ? '' : "\033[0;32m"
+    colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
+    colorcodes['blue']   = monochrome_logs ? '' : "\033[0;34m"
+    colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
+    colorcodes['cyan']   = monochrome_logs ? '' : "\033[0;36m"
+    colorcodes['white']  = monochrome_logs ? '' : "\033[0;37m"
+
+    // Bold
+    colorcodes['bblack']  = monochrome_logs ? '' : "\033[1;30m"
+    colorcodes['bred']    = monochrome_logs ? '' : "\033[1;31m"
+    colorcodes['bgreen']  = monochrome_logs ? '' : "\033[1;32m"
+    colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
+    colorcodes['bblue']   = monochrome_logs ? '' : "\033[1;34m"
+    colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
+    colorcodes['bcyan']   = monochrome_logs ? '' : "\033[1;36m"
+    colorcodes['bwhite']  = monochrome_logs ? '' : "\033[1;37m"
+
+    // Underline
+    colorcodes['ublack']  = monochrome_logs ? '' : "\033[4;30m"
+    colorcodes['ured']    = monochrome_logs ? '' : "\033[4;31m"
+    colorcodes['ugreen']  = monochrome_logs ? '' : "\033[4;32m"
+    colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
+    colorcodes['ublue']   = monochrome_logs ? '' : "\033[4;34m"
+    colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
+    colorcodes['ucyan']   = monochrome_logs ? '' : "\033[4;36m"
+    colorcodes['uwhite']  = monochrome_logs ? '' : "\033[4;37m"
+
+    // High Intensity
+    colorcodes['iblack']  = monochrome_logs ? '' : "\033[0;90m"
+    colorcodes['ired']    = monochrome_logs ? '' : "\033[0;91m"
+    colorcodes['igreen']  = monochrome_logs ? '' : "\033[0;92m"
+    colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
+    colorcodes['iblue']   = monochrome_logs ? '' : "\033[0;94m"
+    colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
+    colorcodes['icyan']   = monochrome_logs ? '' : "\033[0;96m"
+    colorcodes['iwhite']  = monochrome_logs ? '' : "\033[0;97m"
+
+    // Bold High Intensity
+    colorcodes['biblack']  = monochrome_logs ? '' : "\033[1;90m"
+    colorcodes['bired']    = monochrome_logs ? '' : "\033[1;91m"
+    colorcodes['bigreen']  = monochrome_logs ? '' : "\033[1;92m"
+    colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
+    colorcodes['biblue']   = monochrome_logs ? '' : "\033[1;94m"
+    colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
+    colorcodes['bicyan']   = monochrome_logs ? '' : "\033[1;96m"
+    colorcodes['biwhite']  = monochrome_logs ? '' : "\033[1;97m"
+
+    return colorcodes
+}
+
+// Return a single report from an object that may be a Path or List
+//
+def getSingleReport(multiqc_reports) {
+    if (multiqc_reports instanceof Path) {
+        return multiqc_reports
+    } else if (multiqc_reports instanceof List) {
+        if (multiqc_reports.size() == 0) {
+            log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'")
+            return null
+        } else if (multiqc_reports.size() == 1) {
+            return multiqc_reports.first()
+        } else {
+            log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one")
+            return multiqc_reports.first()
+        }
+    } else {
+        return null
+    }
+}
+
+//
+// Construct and send completion email
+//
+def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) {
+
+    // Set up the e-mail variables
+    def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}"
+    if (!workflow.success) {
+        subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}"
+    }
+
+    def summary = [:]
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
+
+    def misc_fields = [:]
+    misc_fields['Date Started']              = workflow.start
+    misc_fields['Date Completed']            = workflow.complete
+    misc_fields['Pipeline script file path'] = workflow.scriptFile
+    misc_fields['Pipeline script hash ID']   = workflow.scriptId
+    if (workflow.repository) {
+        misc_fields['Pipeline repository Git URL']    = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['Pipeline Git branch/tag']        = workflow.revision
+    }
+    misc_fields['Nextflow Version']          = workflow.nextflow.version
+    misc_fields['Nextflow Build']            = workflow.nextflow.build
+    misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+    def email_fields = [:]
+    email_fields['version']      = getWorkflowVersion()
+    email_fields['runName']      = workflow.runName
+    email_fields['success']      = workflow.success
+    email_fields['dateComplete'] = workflow.complete
+    email_fields['duration']     = workflow.duration
+    email_fields['exitStatus']   = workflow.exitStatus
+    email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    email_fields['commandLine']  = workflow.commandLine
+    email_fields['projectDir']   = workflow.projectDir
+    email_fields['summary']      = summary << misc_fields
+
+    // On success try attach the multiqc report
+    def mqc_report = getSingleReport(multiqc_report)
+
+    // Check if we are only sending emails on failure
+    def email_address = email
+    if (!email && email_on_fail && !workflow.success) {
+        email_address = email_on_fail
+    }
+
+    // Render the TXT template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    def tf           = new File("${workflow.projectDir}/assets/email_template.txt")
+    def txt_template = engine.createTemplate(tf).make(email_fields)
+    def email_txt    = txt_template.toString()
+
+    // Render the HTML template
+    def hf            = new File("${workflow.projectDir}/assets/email_template.html")
+    def html_template = engine.createTemplate(hf).make(email_fields)
+    def email_html    = html_template.toString()
+
+    // Render the sendmail template
+    def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit
+    def smail_fields           = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()]
+    def sf                     = new File("${workflow.projectDir}/assets/sendmail_template.txt")
+    def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+    def sendmail_html          = sendmail_template.toString()
+
+    // Send the HTML e-mail
+    def colors = logColours(monochrome_logs) as Map
+    if (email_address) {
+        try {
+            if (plaintext_email) {
+                new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML')
+            }
+            // Try to send HTML e-mail using sendmail
+            def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+            sendmail_tf.withWriter { w -> w << sendmail_html }
+            ['sendmail', '-t'].execute() << sendmail_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-")
+        }
+        catch (Exception msg) {
+            log.debug(msg.toString())
+            log.debug("Trying with mail instead of sendmail")
+            // Catch failures and try with plaintext
+            def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address]
+            mail_cmd.execute() << email_html
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-")
+        }
+    }
+
+    // Write summary e-mail HTML to a file
+    def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
+    output_hf.withWriter { w -> w << email_html }
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html")
+    output_hf.delete()
+
+    // Write summary e-mail TXT to a file
+    def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
+    output_tf.withWriter { w -> w << email_txt }
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt")
+    output_tf.delete()
+}
+
+//
+// Print pipeline summary on completion
+//
+def completionSummary(monochrome_logs=true) {
+    def colors = logColours(monochrome_logs) as Map
+    if (workflow.success) {
+        if (workflow.stats.ignoredCount == 0) {
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-")
+        }
+        else {
+            log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-")
+        }
+    }
+    else {
+        log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-")
+    }
+}
+
+//
+// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack
+//
+def imNotification(summary_params, hook_url) {
+    def summary = [:]
+    summary_params
+        .keySet()
+        .sort()
+        .each { group ->
+            summary << summary_params[group]
+        }
+
+    def misc_fields = [:]
+    misc_fields['start']          = workflow.start
+    misc_fields['complete']       = workflow.complete
+    misc_fields['scriptfile']     = workflow.scriptFile
+    misc_fields['scriptid']       = workflow.scriptId
+    if (workflow.repository) {
+        misc_fields['repository'] = workflow.repository
+    }
+    if (workflow.commitId) {
+        misc_fields['commitid']   = workflow.commitId
+    }
+    if (workflow.revision) {
+        misc_fields['revision']   = workflow.revision
+    }
+    misc_fields['nxf_version']    = workflow.nextflow.version
+    misc_fields['nxf_build']      = workflow.nextflow.build
+    misc_fields['nxf_timestamp']  = workflow.nextflow.timestamp
+
+    def msg_fields = [:]
+    msg_fields['version']      = getWorkflowVersion()
+    msg_fields['runName']      = workflow.runName
+    msg_fields['success']      = workflow.success
+    msg_fields['dateComplete'] = workflow.complete
+    msg_fields['duration']     = workflow.duration
+    msg_fields['exitStatus']   = workflow.exitStatus
+    msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+    msg_fields['errorReport']  = (workflow.errorReport ?: 'None')
+    msg_fields['commandLine']  = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "")
+    msg_fields['projectDir']   = workflow.projectDir
+    msg_fields['summary']      = summary << misc_fields
+
+    // Render the JSON template
+    def engine       = new groovy.text.GStringTemplateEngine()
+    // Different JSON depending on the service provider
+    // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format
+    def json_path     = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json"
+    def hf            = new File("${workflow.projectDir}/assets/${json_path}")
+    def json_template = engine.createTemplate(hf).make(msg_fields)
+    def json_message  = json_template.toString()
+
+    // POST
+    def post = new URL(hook_url).openConnection()
+    post.setRequestMethod("POST")
+    post.setDoOutput(true)
+    post.setRequestProperty("Content-Type", "application/json")
+    post.getOutputStream().write(json_message.getBytes("UTF-8"))
+    def postRC = post.getResponseCode()
+    if (!postRC.equals(200)) {
+        log.warn(post.getErrorStream().getText())
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
new file mode 100644
index 00000000..d08d2434
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml
@@ -0,0 +1,24 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "UTILS_NFCORE_PIPELINE"
+description: Subworkflow with utility functions specific to the nf-core pipeline template
+keywords:
+  - utility
+  - pipeline
+  - initialise
+  - version
+components: []
+input:
+  - nextflow_cli_args:
+      type: list
+      description: |
+        Nextflow CLI positional arguments
+output:
+  - success:
+      type: boolean
+      description: |
+        Dummy output to indicate success
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
+  - "@maxulysse"
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
new file mode 100644
index 00000000..f117040c
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
@@ -0,0 +1,126 @@
+
+nextflow_function {
+
+    name "Test Functions"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Test Function checkConfigProvided") {
+
+        function "checkConfigProvided"
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function checkProfileProvided") {
+
+        function "checkProfileProvided"
+
+        when {
+            function {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function without logColours") {
+
+        function "logColours"
+
+        when {
+            function {
+                """
+                input[0] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function with logColours") {
+        function "logColours"
+
+        when {
+            function {
+                """
+                input[0] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match() }
+            )
+        }
+    }
+
+    test("Test Function getSingleReport with a single file") {
+        function "getSingleReport"
+
+        when {
+            function {
+                """
+                input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert function.result.contains("test.tsv") }
+            )
+        }
+    }
+
+    test("Test Function getSingleReport with multiple files") {
+        function "getSingleReport"
+
+        when {
+            function {
+                """
+                input[0] = [
+                    file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert function.result.contains("test.tsv") },
+                { assert !function.result.contains("network.tsv") },
+                { assert !function.result.contains("expression.tsv") }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
new file mode 100644
index 00000000..02c67014
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -0,0 +1,136 @@
+{
+    "Test Function checkProfileProvided": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:03.360873"
+    },
+    "Test Function checkConfigProvided": {
+        "content": [
+            true
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:59.729647"
+    },
+    "Test Function without logColours": {
+        "content": [
+            {
+                "reset": "",
+                "bold": "",
+                "dim": "",
+                "underlined": "",
+                "blink": "",
+                "reverse": "",
+                "hidden": "",
+                "black": "",
+                "red": "",
+                "green": "",
+                "yellow": "",
+                "blue": "",
+                "purple": "",
+                "cyan": "",
+                "white": "",
+                "bblack": "",
+                "bred": "",
+                "bgreen": "",
+                "byellow": "",
+                "bblue": "",
+                "bpurple": "",
+                "bcyan": "",
+                "bwhite": "",
+                "ublack": "",
+                "ured": "",
+                "ugreen": "",
+                "uyellow": "",
+                "ublue": "",
+                "upurple": "",
+                "ucyan": "",
+                "uwhite": "",
+                "iblack": "",
+                "ired": "",
+                "igreen": "",
+                "iyellow": "",
+                "iblue": "",
+                "ipurple": "",
+                "icyan": "",
+                "iwhite": "",
+                "biblack": "",
+                "bired": "",
+                "bigreen": "",
+                "biyellow": "",
+                "biblue": "",
+                "bipurple": "",
+                "bicyan": "",
+                "biwhite": ""
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:17.969323"
+    },
+    "Test Function with logColours": {
+        "content": [
+            {
+                "reset": "\u001b[0m",
+                "bold": "\u001b[1m",
+                "dim": "\u001b[2m",
+                "underlined": "\u001b[4m",
+                "blink": "\u001b[5m",
+                "reverse": "\u001b[7m",
+                "hidden": "\u001b[8m",
+                "black": "\u001b[0;30m",
+                "red": "\u001b[0;31m",
+                "green": "\u001b[0;32m",
+                "yellow": "\u001b[0;33m",
+                "blue": "\u001b[0;34m",
+                "purple": "\u001b[0;35m",
+                "cyan": "\u001b[0;36m",
+                "white": "\u001b[0;37m",
+                "bblack": "\u001b[1;30m",
+                "bred": "\u001b[1;31m",
+                "bgreen": "\u001b[1;32m",
+                "byellow": "\u001b[1;33m",
+                "bblue": "\u001b[1;34m",
+                "bpurple": "\u001b[1;35m",
+                "bcyan": "\u001b[1;36m",
+                "bwhite": "\u001b[1;37m",
+                "ublack": "\u001b[4;30m",
+                "ured": "\u001b[4;31m",
+                "ugreen": "\u001b[4;32m",
+                "uyellow": "\u001b[4;33m",
+                "ublue": "\u001b[4;34m",
+                "upurple": "\u001b[4;35m",
+                "ucyan": "\u001b[4;36m",
+                "uwhite": "\u001b[4;37m",
+                "iblack": "\u001b[0;90m",
+                "ired": "\u001b[0;91m",
+                "igreen": "\u001b[0;92m",
+                "iyellow": "\u001b[0;93m",
+                "iblue": "\u001b[0;94m",
+                "ipurple": "\u001b[0;95m",
+                "icyan": "\u001b[0;96m",
+                "iwhite": "\u001b[0;97m",
+                "biblack": "\u001b[1;90m",
+                "bired": "\u001b[1;91m",
+                "bigreen": "\u001b[1;92m",
+                "biyellow": "\u001b[1;93m",
+                "biblue": "\u001b[1;94m",
+                "bipurple": "\u001b[1;95m",
+                "bicyan": "\u001b[1;96m",
+                "biwhite": "\u001b[1;97m"
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:21.714424"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
new file mode 100644
index 00000000..8940d32d
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
@@ -0,0 +1,29 @@
+nextflow_workflow {
+
+    name "Test Workflow UTILS_NFCORE_PIPELINE"
+    script "../main.nf"
+    config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config"
+    workflow "UTILS_NFCORE_PIPELINE"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "utils_nfcore_pipeline"
+    tag "subworkflows/utils_nfcore_pipeline"
+
+    test("Should run without failures") {
+
+        when {
+            workflow {
+                """
+                input[0] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
new file mode 100644
index 00000000..859d1030
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    true
+                ],
+                "valid_config": [
+                    true
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
new file mode 100644
index 00000000..d0a926bf
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config
@@ -0,0 +1,9 @@
+manifest {
+    name            = 'nextflow_workflow'
+    author          = """nf-core"""
+    homePage        = 'https://127.0.0.1'
+    description     = """Dummy pipeline"""
+    nextflowVersion  = '!>=23.04.0'
+    version         = '9.9.9'
+    doi             = 'https://doi.org/10.5281/zenodo.5070524'
+}

From a9e6512a83ec47c7030ce612b48e60738f1d5882 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 15 May 2025 11:41:47 +1000
Subject: [PATCH 61/88] change version collection

---
 workflows/sash.nf | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 1ce4d20b..50379776 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -49,6 +49,8 @@ include { BOLT_SV_SOMATIC_PRIORITISE } from '../modules/local/bolt/sv_somatic/pr
 include { ESVEE_CALL                 } from '../modules/local/esvee/call/main'
 include { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
 
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
+
 include { LINX_ANNOTATION            } from '../subworkflows/local/linx_annotation'
 include { LINX_PLOTTING              } from '../subworkflows/local/linx_plotting'
 include { PREPARE_INPUT              } from '../subworkflows/local/prepare_input'
@@ -539,11 +541,15 @@ workflow SASH {
 
 
     //
-    // Collect software versions
+    // TASK: Aggregate software versions
     //
-    CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique().collectFile(name: 'collated_versions.yml')
-    )
+    softwareVersionsToYAML(ch_versions)
+        .collectFile(
+            storeDir: "${params.outdir}/pipeline_info",
+            name: 'software_versions.yml',
+            sort: true,
+            newLine: true,
+        )
 
 }
 

From 6af54578b9ef7275e9b5ab25148920bf589133c0 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 15 May 2025 14:56:08 +1000
Subject: [PATCH 62/88] fix meta

---
 subworkflows/local/prepare_input.nf | 1 +
 workflows/sash.nf                   | 6 +-----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index 49ccf207..b81e1329 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -57,6 +57,7 @@ workflow PREPARE_INPUT {
                 id: meta.id,
                 tumor_id: meta.tumor_id,
                 normal_id: meta.normal_id,
+                sample_id: meta.tumor_id
             ]
 
             def base = file(meta.oncoanalyser_dir).toUriString()
diff --git a/workflows/sash.nf b/workflows/sash.nf
index 50379776..731b36bf 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -49,8 +49,6 @@ include { BOLT_SV_SOMATIC_PRIORITISE } from '../modules/local/bolt/sv_somatic/pr
 include { ESVEE_CALL                 } from '../modules/local/esvee/call/main'
 include { PAVE_SOMATIC               } from '../modules/local/pave/somatic/main'
 
-include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-
 include { LINX_ANNOTATION            } from '../subworkflows/local/linx_annotation'
 include { LINX_PLOTTING              } from '../subworkflows/local/linx_plotting'
 include { PREPARE_INPUT              } from '../subworkflows/local/prepare_input'
@@ -63,7 +61,7 @@ include { PURPLE_CALLING             } from '../subworkflows/local/purple_callin
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
+include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -430,8 +428,6 @@ workflow SASH {
     // Generate the cancer report
     //
 
-    // channel: [ meta, 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 ]
     ch_cancer_report_inputs = WorkflowSash.groupByMeta(
         ch_smlv_somatic_out,

From 7350545a33a32af2ebec36993be6e1e3c1f13158 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 16 May 2025 15:15:46 +1000
Subject: [PATCH 63/88] fix channel meta for stub and standar run

---
 workflows/sash.nf | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 731b36bf..f9e97ab4 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -135,6 +135,7 @@ workflow SASH {
                 id: meta.id,
                 tumor_id: meta.tumor_id,
                 normal_id: meta.normal_id,
+                sample_id: meta.tumor_id
             ]
             return [meta_bolt, *it[1..-1]]
         }
@@ -233,6 +234,9 @@ workflow SASH {
 
     ch_versions = ch_versions.mix(ESVEE_CALL.out.versions)
 
+    ch_esvee_somatic_out = WorkflowSash.restoreMeta(ESVEE_CALL.out.somatic_vcf, ch_inputs)
+    ch_esvee_germline_out =  WorkflowSash.restoreMeta(ESVEE_CALL.out.germline_vcf, ch_inputs)
+
 
 
 
@@ -254,8 +258,8 @@ workflow SASH {
         //ch_smlv_germline_out,
         ch_smlv_germline_out.map { meta, vcf -> return [meta, []] },
 
-        ESVEE_CALL.out.somatic_vcf,
-        ESVEE_CALL.out.germline_vcf,
+        ch_esvee_somatic_out,
+        ch_esvee_germline_out,
         genome.fasta,
         genome.version,
         genome.fai,
@@ -268,6 +272,8 @@ workflow SASH {
         hmf_data.purple_germline_del,
     )
 
+    ch_versions = ch_versions.mix(PURPLE_CALLING.out.versions)
+
 
 
 

From fb02a3140c4104b403ca298f6d166539a954b50c Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 16 May 2025 15:16:07 +1000
Subject: [PATCH 64/88] remove deprecated modules

---
 .../custom/dumpsoftwareversions/main.nf       |  31 ------
 .../custom/dumpsoftwareversions/meta.yml      |  36 -------
 .../templates/dumpsoftwareversions.py         | 102 ------------------
 modules/nf-core/fastqc/main.nf                |  51 ---------
 modules/nf-core/fastqc/meta.yml               |  52 ---------
 modules/nf-core/multiqc/main.nf               |  53 ---------
 modules/nf-core/multiqc/meta.yml              |  56 ----------
 7 files changed, 381 deletions(-)
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf
 delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml
 delete mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
 delete mode 100644 modules/nf-core/fastqc/main.nf
 delete mode 100644 modules/nf-core/fastqc/meta.yml
 delete mode 100644 modules/nf-core/multiqc/main.nf
 delete mode 100644 modules/nf-core/multiqc/meta.yml

diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
deleted file mode 100644
index f3b3d8a8..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_single'
-
-    // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda "bioconda::multiqc=1.14"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
-
-    input:
-    path versions
-
-    output:
-    path "software_versions.yml"    , emit: yml
-    path "software_versions_mqc.yml", emit: mqc_yml
-    path "versions.yml"             , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    template 'dumpsoftwareversions.py'
-
-    stub:
-    """
-    touch software_versions.yml
-    touch software_versions_mqc.yml
-    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
-    """
-}
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
deleted file mode 100644
index c32657de..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ /dev/null
@@ -1,36 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
-name: custom_dumpsoftwareversions
-description: Custom module used to dump software versions within the nf-core pipeline template
-keywords:
-  - custom
-  - dump
-  - version
-tools:
-  - custom:
-      description: Custom module used to dump software versions within the nf-core pipeline template
-      homepage: https://github.com/nf-core/tools
-      documentation: https://github.com/nf-core/tools
-      licence: ["MIT"]
-input:
-  - versions:
-      type: file
-      description: YML file containing software versions
-      pattern: "*.yml"
-
-output:
-  - yml:
-      type: file
-      description: Standard YML file containing software versions
-      pattern: "software_versions.yml"
-  - mqc_yml:
-      type: file
-      description: MultiQC custom content YML file containing software versions
-      pattern: "software_versions_mqc.yml"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@drpatelh"
-  - "@grst"
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
deleted file mode 100755
index e55b8d43..00000000
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ /dev/null
@@ -1,102 +0,0 @@
-#!/usr/bin/env python
-
-
-"""Provide functions to merge multiple versions.yml files."""
-
-
-import platform
-from textwrap import dedent
-
-import yaml
-
-
-def _make_versions_html(versions):
-    """Generate a tabular HTML output of all versions for MultiQC."""
-    html = [
-        dedent(
-            """\\
-            <style>
-            #nf-core-versions tbody:nth-child(even) {
-                background-color: #f2f2f2;
-            }
-            </style>
-            <table class="table" style="width:100%" id="nf-core-versions">
-                <thead>
-                    <tr>
-                        <th> Process Name </th>
-                        <th> Software </th>
-                        <th> Version  </th>
-                    </tr>
-                </thead>
-            """
-        )
-    ]
-    for process, tmp_versions in sorted(versions.items()):
-        html.append("<tbody>")
-        for i, (tool, version) in enumerate(sorted(tmp_versions.items())):
-            html.append(
-                dedent(
-                    f"""\\
-                    <tr>
-                        <td><samp>{process if (i == 0) else ''}</samp></td>
-                        <td><samp>{tool}</samp></td>
-                        <td><samp>{version}</samp></td>
-                    </tr>
-                    """
-                )
-            )
-        html.append("</tbody>")
-    html.append("</table>")
-    return "\\n".join(html)
-
-
-def main():
-    """Load all version files and generate merged output."""
-    versions_this_module = {}
-    versions_this_module["${task.process}"] = {
-        "python": platform.python_version(),
-        "yaml": yaml.__version__,
-    }
-
-    with open("$versions") as f:
-        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-    # aggregate versions by the module name (derived from fully-qualified process name)
-    versions_by_module = {}
-    for process, process_versions in versions_by_process.items():
-        module = process.split(":")[-1]
-        try:
-            if versions_by_module[module] != process_versions:
-                raise AssertionError(
-                    "We assume that software versions are the same between all modules. "
-                    "If you see this error-message it means you discovered an edge-case "
-                    "and should open an issue in nf-core/tools. "
-                )
-        except KeyError:
-            versions_by_module[module] = process_versions
-
-    versions_by_module["Workflow"] = {
-        "Nextflow": "$workflow.nextflow.version",
-        "$workflow.manifest.name": "$workflow.manifest.version",
-    }
-
-    versions_mqc = {
-        "id": "software_versions",
-        "section_name": "${workflow.manifest.name} Software Versions",
-        "section_href": "https://github.com/${workflow.manifest.name}",
-        "plot_type": "html",
-        "description": "are collected at run time from the software output.",
-        "data": _make_versions_html(versions_by_module),
-    }
-
-    with open("software_versions.yml", "w") as f:
-        yaml.dump(versions_by_module, f, default_flow_style=False)
-    with open("software_versions_mqc.yml", "w") as f:
-        yaml.dump(versions_mqc, f, default_flow_style=False)
-
-    with open("versions.yml", "w") as f:
-        yaml.dump(versions_this_module, f, default_flow_style=False)
-
-
-if __name__ == "__main__":
-    main()
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
deleted file mode 100644
index 9ae58381..00000000
--- a/modules/nf-core/fastqc/main.nf
+++ /dev/null
@@ -1,51 +0,0 @@
-process FASTQC {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "bioconda::fastqc=0.11.9"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'quay.io/biocontainers/fastqc:0.11.9--0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    // Make list of old name and new name pairs to use for renaming in the bash while loop
-    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
-    def rename_to = old_new_pairs*.join(' ').join(' ')
-    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
-    """
-    printf "%s %s\\n" $rename_to | while read old_name new_name; do
-        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
-    done
-    fastqc $args --threads $task.cpus $renamed_files
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.html
-    touch ${prefix}.zip
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
deleted file mode 100644
index 4da5bb5a..00000000
--- a/modules/nf-core/fastqc/meta.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-name: fastqc
-description: Run FastQC on sequenced reads
-keywords:
-  - quality control
-  - qc
-  - adapters
-  - fastq
-tools:
-  - fastqc:
-      description: |
-        FastQC gives general quality metrics about your reads.
-        It provides information about the quality score distribution
-        across your reads, the per base sequence content (%A/C/G/T).
-        You get information about adapter contamination and other
-        overrepresented sequences.
-      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-      licence: ["GPL-2.0-only"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
-  - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@grst"
-  - "@ewels"
-  - "@FelixKrueger"
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
deleted file mode 100644
index 4b604749..00000000
--- a/modules/nf-core/multiqc/main.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-process MULTIQC {
-    label 'process_single'
-
-    conda "bioconda::multiqc=1.14"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
-
-    input:
-    path  multiqc_files, stageAs: "?/*"
-    path(multiqc_config)
-    path(extra_multiqc_config)
-    path(multiqc_logo)
-
-    output:
-    path "*multiqc_report.html", emit: report
-    path "*_data"              , emit: data
-    path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def config = multiqc_config ? "--config $multiqc_config" : ''
-    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
-    """
-    multiqc \\
-        --force \\
-        $args \\
-        $config \\
-        $extra_config \\
-        .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
-    """
-
-    stub:
-    """
-    touch multiqc_data
-    touch multiqc_plots
-    touch multiqc_report.html
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
deleted file mode 100644
index f93b5ee5..00000000
--- a/modules/nf-core/multiqc/meta.yml
+++ /dev/null
@@ -1,56 +0,0 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
-name: MultiQC
-description: Aggregate results from bioinformatics analyses across many samples into a single report
-keywords:
-  - QC
-  - bioinformatics tools
-  - Beautiful stand-alone HTML report
-tools:
-  - multiqc:
-      description: |
-        MultiQC searches a given directory for analysis logs and compiles a HTML report.
-        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
-      homepage: https://multiqc.info/
-      documentation: https://multiqc.info/docs/
-      licence: ["GPL-3.0-or-later"]
-
-input:
-  - multiqc_files:
-      type: file
-      description: |
-        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
-  - multiqc_config:
-      type: file
-      description: Optional config yml for MultiQC
-      pattern: "*.{yml,yaml}"
-  - extra_multiqc_config:
-      type: file
-      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
-      pattern: "*.{yml,yaml}"
-  - multiqc_logo:
-      type: file
-      description: Optional logo file for MultiQC
-      pattern: "*.{png}"
-
-output:
-  - report:
-      type: file
-      description: MultiQC report file
-      pattern: "multiqc_report.html"
-  - data:
-      type: directory
-      description: MultiQC data dir
-      pattern: "multiqc_data"
-  - plots:
-      type: file
-      description: Plots created by MultiQC
-      pattern: "*_data"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@abhi18av"
-  - "@bunop"
-  - "@drpatelh"
-  - "@jfy133"

From 43d18cef634b87991ae13e72ccf6bf98bd6516c5 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 16 May 2025 15:19:30 +1000
Subject: [PATCH 65/88] upgrade gpgr container

---
 modules/local/bolt/other/cancer_report/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index ab41d0bf..e677c51f 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee-2'
+    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee-3'
 
     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)

From 3112089089c9ad492e39943ea04c6f148baaa49c Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 22 May 2025 10:53:38 +1000
Subject: [PATCH 66/88] update changelog

---
 CHANGELOG.md                         | 40 ++++++++++++++++++++++++++++
 subworkflows/local/purple_calling.nf |  4 +--
 2 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d88a7205..49cbc8b8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,3 +14,43 @@ Initial release of umccr/sash, created with the [nf-core](https://nf-co.re/) tem
 ### `Dependencies`
 
 ### `Deprecated`
+
+## [0.6.0] – 2025-05-19
+
+### Added
+
+- _none_
+
+### Changed
+
+- SV caller switched GRIPSS → eSVe
+- Cancer-report Structural Variants plot: `SR`→`SF`, `PR`→`DF`
+- Linx upgraded 1.25 → 2.0
+- Purple upgraded 4.0.1 → 4.1.0
+- Bolt & GPGR updated for the adpat to above change
+
+### Removed
+
+- Kataegis module
+- CHORD HRD metrics
+
+### Deprecated
+
+- Metric aliases `SR`, `PR`
+
+### Fixed
+
+- _none_
+
+### Security
+
+- _none_
+
+### Dependencies
+
+| 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/subworkflows/local/purple_calling.nf b/subworkflows/local/purple_calling.nf
index ef73140c..444d0b68 100644
--- a/subworkflows/local/purple_calling.nf
+++ b/subworkflows/local/purple_calling.nf
@@ -33,7 +33,7 @@ workflow PURPLE_CALLING {
         ch_versions = Channel.empty()
 
         // Collect inputs
-        // channel: [ meta, amber_dir, cobalt_dir, sv_somatic_vcf, sv_somatic_tbi, sv_somatic_unfiltered_vcf, sv_somatic_unfiltered_tbi, sv_germline_vcf, sv_germline_tbi, smlv_somatic_vcf, smlv_germline_vcf ]
+        // channel: [ meta, amber_dir, cobalt_dir, sv_somatic_vcf, sv_somatic_tbi, sv_germline_vcf, sv_germline_tbi, smlv_somatic_vcf, smlv_germline_vcf ]
         ch_purple_inputs_source = WorkflowSash.groupByMeta(
             // Required inputs
             ch_amber,
@@ -47,7 +47,7 @@ workflow PURPLE_CALLING {
         )
 
         // Create process-specific meta
-        // channel: [ meta_purple, amber_dir, cobalt_dir, sv_somatic_vcf, sv_somatic_tbi, sv_somatic_unfiltered_vcf, sv_somatic_unfilt_vcf, sv_germline_tbi, smlv_somatic_vcf, smlv_germline_vcf ]
+        // channel: [ meta_purple, amber_dir, cobalt_dir, sv_somatic_vcf, sv_somatic_tbi, sv_germline_tbi, smlv_somatic_vcf, smlv_germline_vcf ]
         ch_purple_inputs = ch_purple_inputs_source
             .map {
                 def meta = it[0]

From 3afbc68bb1b5dbb6ad7a33a7aec11bd783ad3380 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 22 May 2025 10:54:48 +1000
Subject: [PATCH 67/88] remove deprecated tool versionning  collection

---
 conf/base.config                                    | 3 ---
 conf/modules.config                                 | 8 --------
 modules/nf-core/custom/dumpsoftwareversions/main.nf | 0
 3 files changed, 11 deletions(-)
 create mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf

diff --git a/conf/base.config b/conf/base.config
index 39c4800a..65e095e5 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -53,7 +53,4 @@ process {
         maxRetries    = 2
     }
 
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index c8777ec1..b729e3af 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -212,12 +212,4 @@ process {
         ]
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
new file mode 100644
index 00000000..e69de29b

From 01a0001b6a698ee2f795663a9fe7b2e3939ceae7 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 27 May 2025 10:54:27 +1000
Subject: [PATCH 68/88] upadte pave

---
 modules/local/pave/Dockerfile      | 2 +-
 modules/local/pave/somatic/main.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/pave/Dockerfile b/modules/local/pave/Dockerfile
index 47d89500..d0b4fe12 100644
--- a/modules/local/pave/Dockerfile
+++ b/modules/local/pave/Dockerfile
@@ -7,7 +7,7 @@ RUN \
     zlib && \
   micromamba clean --all --yes
 
-FROM quay.io/biocontainers/hmftools-pave:1.6--hdfd78af_0
+FROM quay.io/biocontainers/hmftools-pave:1.7--hdfd78af_0
 
 COPY --from=build /env/ /env/
 
diff --git a/modules/local/pave/somatic/main.nf b/modules/local/pave/somatic/main.nf
index b17725fb..0a7c7954 100644
--- a/modules/local/pave/somatic/main.nf
+++ b/modules/local/pave/somatic/main.nf
@@ -2,7 +2,7 @@ process PAVE_SOMATIC {
     tag "${meta.id}"
     label 'process_medium'
 
-    container 'docker.io/scwatts/hmftools-pave:1.6--0'
+    container 'docker.io/qclayssen/hmftools-pave:1.7--hdfd78af_0'
 
     input:
     tuple val(meta), path(vcf), path(tbi)

From 9cf9f5e029c57d89edb1f1f164a51ea6557b054e Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 27 May 2025 15:10:31 +1000
Subject: [PATCH 69/88] update container for esvee

---
 modules/local/bolt/other/cancer_report/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index e677c51f..0be6eb3d 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee-3'
+    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee-4'
 
     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)

From ee113189d839200b69e6171f9e8d2d2ad0f907cb Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 29 May 2025 09:48:13 +1000
Subject: [PATCH 70/88] update cancer report container

---
 modules/local/bolt/other/cancer_report/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index 0be6eb3d..cb02bbc7 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee-4'
+    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee-5'
 
     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)

From cd3f6640bc338a18a9158b4afcfd101946dedba3 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 29 May 2025 14:27:23 +1000
Subject: [PATCH 71/88] Remove deprecated module trace

---
 modules.json | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/modules.json b/modules.json
index 42c1b398..8995535e 100644
--- a/modules.json
+++ b/modules.json
@@ -5,11 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
-                        "installed_by": ["modules"]
-                    },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",

From 3da7b3e9dcab2079bd39d9765648b1b415f09984 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 29 May 2025 14:27:34 +1000
Subject: [PATCH 72/88] Upadate changelog for MSI

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 49cbc8b8..dbfbe71a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,6 +33,7 @@ Initial release of umccr/sash, created with the [nf-core](https://nf-co.re/) tem
 
 - Kataegis module
 - CHORD HRD metrics
+- MSI load and status from purple
 
 ### Deprecated
 

From 14f1ab8eb7cdcc6c9a14a2c56a1366a8cb4af573 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 2 Jun 2025 12:13:28 +1000
Subject: [PATCH 73/88] fix documentation

---
 subworkflows/local/prepare_input.nf | 41 +++++++++++++++++++++--------
 1 file changed, 30 insertions(+), 11 deletions(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index b81e1329..b6d0c8e9 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -3,7 +3,9 @@ workflow PREPARE_INPUT {
         ch_samplesheet
 
     main:
-        def ch_metas = Channel.of(ch_samplesheet)
+        // Parse samplesheet and group entries by sample ID
+        // channel: [ meta ]
+        ch_metas = Channel.of(ch_samplesheet)
             .splitCsv(header: true)
             .map { [it.id, it] }
             .groupTuple()
@@ -40,18 +42,25 @@ workflow PREPARE_INPUT {
                 return meta
             }
 
-        // map oncoanalyser assets and DRAGEN outputs into channels
-        def ch_amber = ch_metas.map { meta ->
+        // Map oncoanalyser assets and DRAGEN outputs into channels
+
+        // AMBER: copy number segmentation data
+        // channel: [ meta, amber_dir ]
+        ch_amber = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             return [meta, "${base}/amber/"]
         }
 
-        def ch_cobalt = ch_metas.map { meta ->
+        // COBALT: read depth ratio data
+        // channel: [ meta, cobalt_dir ]
+        ch_cobalt = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             return [meta, "${base}/cobalt/"]
         }
 
-        def ch_call_inputs = ch_metas.map { meta ->
+        // eSVee: structural variant calling inputs
+        // channel: [ meta_esvee, esvee_ref_depth_vcf, esvee_prep_dir ]
+        ch_call_inputs = ch_metas.map { meta ->
             def meta_esvee = [
                 key: meta.id,
                 id: meta.id,
@@ -66,28 +75,38 @@ workflow PREPARE_INPUT {
             return [meta_esvee, vcf, dir]
         }
 
-        def ch_sage_somatic = ch_metas.map { meta ->
+        // SAGE: somatic small variant calls
+        // channel: [ meta, sage_somatic_vcf, sage_somatic_tbi ]
+        ch_sage_somatic = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             def vcf = "${base}/sage/somatic/${meta.tumor_id}.sage.somatic.vcf.gz"
             return [meta, vcf, "${vcf}.tbi"]
         }
 
-        def ch_virusbreakend = ch_metas.map { meta ->
+        // VirusBreakend: viral integration detection
+        // channel: [ meta, virusbreakend_dir ]
+        ch_virusbreakend = ch_metas.map { meta ->
             def base = file(meta.oncoanalyser_dir).toUriString()
             return [meta, "${base}/virusbreakend/"]
         }
 
-        def ch_input_hrd = ch_metas.map { meta ->
+        // HRD: homologous recombination deficiency scores
+        // channel: [ meta, hrdscore_csv ]
+        ch_input_hrd = ch_metas.map { meta ->
             def base = file(meta.dragen_somatic_dir).toUriString()
             return [meta, "${base}/${meta.tumor_id}.hrdscore.csv"]
         }
 
-        def ch_input_vcf_germline = ch_metas.map { meta ->
+        // DRAGEN germline variants
+        // channel: [ meta, dragen_germline_vcf ]
+        ch_input_vcf_germline = ch_metas.map { meta ->
             def base = file(meta.dragen_germline_dir).toUriString()
             return [meta, "${base}/${meta.normal_id}.hard-filtered.vcf.gz"]
         }
 
-        def ch_input_vcf_somatic = ch_metas.map { meta ->
+        // DRAGEN somatic variants
+        // channel: [ meta, dragen_somatic_vcf, dragen_somatic_tbi ]
+        ch_input_vcf_somatic = ch_metas.map { meta ->
             def base = file(meta.dragen_somatic_dir).toUriString()
             def vcf = "${base}/${meta.tumor_id}.hard-filtered.vcf.gz"
             return [meta, vcf, "${vcf}.tbi"]
@@ -108,5 +127,5 @@ workflow PREPARE_INPUT {
         vcf_somatic = ch_input_vcf_somatic   // channel: [ meta, dragen_somatic_vcf, dragen_somatic_tbi ]
 
         // eSVee inputs
-        call_inputs = ch_call_inputs             // channel: [ meta, esvee_prep_dir, esvee_ref_depth_vcf ]
+        call_inputs = ch_call_inputs             // channel: [ meta_esvee, esvee_ref_depth_vcf, esvee_prep_dir ]
 }

From 6023723f969833f9ea596d3284769479ff0f916d Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 2 Jun 2025 12:17:48 +1000
Subject: [PATCH 74/88] linting

---
 subworkflows/local/prepare_input.nf | 30 ++++++++++++++---------------
 1 file changed, 14 insertions(+), 16 deletions(-)

diff --git a/subworkflows/local/prepare_input.nf b/subworkflows/local/prepare_input.nf
index b6d0c8e9..f2a74d70 100644
--- a/subworkflows/local/prepare_input.nf
+++ b/subworkflows/local/prepare_input.nf
@@ -112,20 +112,18 @@ workflow PREPARE_INPUT {
             return [meta, vcf, "${vcf}.tbi"]
         }
     emit:
-        // Meta information for each sample
-        metas = ch_metas                   // channel: [ meta ]
-
-        // Oncoanalyser inputs
-        amber = ch_amber                   // channel: [ meta, amber_dir ]
-        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 ]
-
-        // DRAGEN inputs
-        hrd = ch_input_hrd                 // channel: [ meta, hrdscore_csv ]
-        vcf_germline = ch_input_vcf_germline // channel: [ meta, dragen_germline_vcf ]
-        vcf_somatic = ch_input_vcf_somatic   // channel: [ meta, dragen_somatic_vcf, dragen_somatic_tbi ]
-
-        // eSVee inputs
-        call_inputs = ch_call_inputs             // channel: [ meta_esvee, esvee_ref_depth_vcf, esvee_prep_dir ]
+        // Sample metadata
+        metas            = ch_metas                   // channel: [ meta ]
+
+        // oncoanalyser channels
+        amber            = ch_amber                   // channel: [ meta, amber_dir ]
+        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 ]
+        call_inputs      = ch_call_inputs             // channel: [ meta_esvee, esvee_ref_depth_vcf, esvee_prep_dir ]
+
+        // DRAGEN channels
+        hrd              = ch_input_hrd               // channel: [ meta, hrdscore_csv ]
+        vcf_germline     = ch_input_vcf_germline      // channel: [ meta, dragen_germline_vcf ]
+        vcf_somatic      = ch_input_vcf_somatic       // channel: [ meta, dragen_somatic_vcf, dragen_somatic_tbi ]
 }

From 757c2bd8c5b042f4e8e264b0c6f3b93528a02d0a Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 2 Jun 2025 12:34:43 +1000
Subject: [PATCH 75/88] tidy up channel

---
 workflows/sash.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index f9e97ab4..596f2daa 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -91,15 +91,13 @@ workflow SASH {
     ch_cobalt              = PREPARE_INPUT.out.cobalt            // channel: [ meta, cobalt_dir ]
     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_prep_dir, esvee_ref_depth_vcf ]
 
     // DRAGEN inputs
     ch_input_hrd           = PREPARE_INPUT.out.hrd               // channel: [ meta, hrdscore_csv ]
     ch_input_vcf_germline  = PREPARE_INPUT.out.vcf_germline      // channel: [ meta, dragen_germline_vcf ]
     ch_input_vcf_somatic   = PREPARE_INPUT.out.vcf_somatic       // channel: [ meta, dragen_somatic_vcf, dragen_somatic_tbi ]
 
-    // eSVee inputs
-    ch_call_inputs         = PREPARE_INPUT.out.call_inputs       // channel: [ meta, esvee_prep_dir, esvee_ref_depth_vcf ]
-
 
 
 

From 35e3a349d8e8bd0e6286f651f779031707ae8f8e Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Mon, 2 Jun 2025 12:47:52 +1000
Subject: [PATCH 76/88] tidy up

---
 workflows/sash.nf | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/workflows/sash.nf b/workflows/sash.nf
index 596f2daa..12080847 100644
--- a/workflows/sash.nf
+++ b/workflows/sash.nf
@@ -84,14 +84,15 @@ workflow SASH {
     PREPARE_INPUT(
         file(params.input),
     )
-    ch_inputs = PREPARE_INPUT.out.metas            // channel: [ meta ]
+
+    ch_inputs              = PREPARE_INPUT.out.metas             // channel: [ meta ]
 
     // OncoAnalyser inputs
     ch_amber               = PREPARE_INPUT.out.amber             // channel: [ meta, amber_dir ]
     ch_cobalt              = PREPARE_INPUT.out.cobalt            // channel: [ meta, cobalt_dir ]
     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_prep_dir, esvee_ref_depth_vcf ]
+    ch_call_inputs         = PREPARE_INPUT.out.call_inputs       // channel: [ meta_esvee, esvee_ref_depth_vcf, esvee_prep_dir ]
 
     // DRAGEN inputs
     ch_input_hrd           = PREPARE_INPUT.out.hrd               // channel: [ meta, hrdscore_csv ]

From ac5241f3bca0f4c2c0b892e01813fe6c9429dbc6 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Tue, 3 Jun 2025 09:26:11 +1000
Subject: [PATCH 77/88] remove deprecated module

---
 modules/local/gripss/Dockerfile        | 15 ------
 modules/local/gripss/germline/main.nf  | 59 ---------------------
 modules/local/gripss/germline/meta.yml | 68 ------------------------
 modules/local/gripss/somatic/main.nf   | 64 -----------------------
 modules/local/gripss/somatic/meta.yml  | 71 --------------------------
 5 files changed, 277 deletions(-)
 delete mode 100644 modules/local/gripss/Dockerfile
 delete mode 100644 modules/local/gripss/germline/main.nf
 delete mode 100644 modules/local/gripss/germline/meta.yml
 delete mode 100644 modules/local/gripss/somatic/main.nf
 delete mode 100644 modules/local/gripss/somatic/meta.yml

diff --git a/modules/local/gripss/Dockerfile b/modules/local/gripss/Dockerfile
deleted file mode 100644
index 075afea8..00000000
--- a/modules/local/gripss/Dockerfile
+++ /dev/null
@@ -1,15 +0,0 @@
-FROM mambaorg/micromamba:1.5.7 as build
-
-USER root
-
-RUN \
-  micromamba create -y -p /env/ -c bioconda -c conda-forge \
-    zlib && \
-  micromamba clean --all --yes
-
-FROM quay.io/biocontainers/hmftools-gripss:2.4--hdfd78af_0
-
-COPY --from=build /env/ /env/
-
-ENV PATH="/env/bin:${PATH}"
-ENV LD_LIBRARY_PATH="/env/lib/:${LD_LIBRARY_PATH}"
diff --git a/modules/local/gripss/germline/main.nf b/modules/local/gripss/germline/main.nf
deleted file mode 100644
index 444ee912..00000000
--- a/modules/local/gripss/germline/main.nf
+++ /dev/null
@@ -1,59 +0,0 @@
-process GRIPSS_GERMLINE {
-    tag "${meta.id}"
-    label 'process_low'
-
-    container 'docker.io/scwatts/hmftools-gripss:2.4--0'
-
-    input:
-    tuple val(meta), path(gridss_vcf)
-    path genome_fasta
-    val genome_ver
-    path genome_fai
-    path pon_breakends
-    path pon_breakpoints
-    path known_fusions
-    path repeatmasker_annotations
-
-    output:
-    tuple val(meta), path('*.filtered.germline.vcf.gz'), path('*.filtered.germline.vcf.gz.tbi'), emit: vcf
-    tuple val(meta), path('*gripss.germline.vcf.gz'), path('*gripss.germline.vcf.gz.tbi')      , emit: vcf_unfiltered
-    path 'versions.yml'                                                                        , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-
-    """
-    gripss \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
-        ${args} \\
-        -sample ${meta.normal_id} \\
-        -reference ${meta.tumor_id} \\
-        -vcf ${gridss_vcf} \\
-        -germline \\
-        -ref_genome ${genome_fasta} \\
-        -ref_genome_version ${genome_ver} \\
-        -pon_sgl_file ${pon_breakends} \\
-        -pon_sv_file ${pon_breakpoints} \\
-        -known_hotspot_file ${known_fusions} \\
-        -repeat_mask_file ${repeatmasker_annotations} \\
-        -output_id germline \\
-        -output_dir ./
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gripss: \$(gripss -version | sed 's/^.* //')
-    END_VERSIONS
-    """
-
-    stub:
-    """
-    touch ${meta.normal_id}.gripss.filtered.germline.vcf.gz
-    touch ${meta.normal_id}.gripss.filtered.germline.vcf.gz.tbi
-    touch ${meta.normal_id}.gripss.germline.vcf.gz
-    touch ${meta.normal_id}.gripss.germline.vcf.gz.tbi
-    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
-    """
-}
diff --git a/modules/local/gripss/germline/meta.yml b/modules/local/gripss/germline/meta.yml
deleted file mode 100644
index 03ae9328..00000000
--- a/modules/local/gripss/germline/meta.yml
+++ /dev/null
@@ -1,68 +0,0 @@
-name: gripss_germline
-description: Filter and process GRIDSS germline structural variants
-keywords:
-  - sv
-  - filtering
-  - germline
-tools:
-  - gripss:
-      description: Apply filtering and post-processing to GRIDSS structural variants.
-      homepage: https://github.com/hartwigmedical/hmftools/tree/master/gripss
-      documentation: https://github.com/hartwigmedical/hmftools/tree/master/gripss
-      licence: ["GPL v3"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [id: 'sample_id', normal_id: 'normal_name']
-  - gridss_vcf:
-      type: file
-      description: VCF file
-      pattern: "*.{vcf.gz}"
-  - genome_fasta:
-      type: file
-      description: Reference genome assembly FASTA file
-      pattern: "*.{fa,fasta}"
-  - genome_ver:
-      type: string
-      description: Reference genome version
-  - genome_fai:
-      type: file
-      description: Reference genome assembly fai file
-      pattern: "*.{fai}"
-  - pon_breakends:
-      type: file
-      description: GRIDSS breakend PON file
-      pattern: "*.{bed.gz}"
-  - pon_breakpoints:
-      type: file
-      description: GRIDSS breakpoint PON file
-      pattern: "*.{bedpe.gz}"
-  - known_fusions:
-      type: file
-      description: HMF Known Fusions file
-      pattern: "*.{bedpe}"
-  - repeatmasker_annotations:
-      type: file
-      description: RepeatMasker annotations file
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [id: 'sample_id', normal_id: 'normal_name']
-  - vcf:
-      type: list
-      description: Filtered VCF file and index file
-      pattern: "*.{vcf.gz,vcf.gz.tbi}"
-  - vcf_unfiltered:
-      type: list
-      description: Unfiltered VCF file and index file
-      pattern: "*.{vcf.gz,vcf.gz.tbi}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@scwatts"
diff --git a/modules/local/gripss/somatic/main.nf b/modules/local/gripss/somatic/main.nf
deleted file mode 100644
index 47bd1c41..00000000
--- a/modules/local/gripss/somatic/main.nf
+++ /dev/null
@@ -1,64 +0,0 @@
-process GRIPSS_SOMATIC {
-    tag "${meta.id}"
-    label 'process_low'
-
-    container 'docker.io/scwatts/hmftools-gripss:2.4--0'
-
-    input:
-    tuple val(meta), path(gridss_vcf)
-    path genome_fasta
-    val genome_ver
-    path genome_fai
-    path pon_breakends
-    path pon_breakpoints
-    path known_fusions
-    path repeatmasker_annotations
-    path target_region_bed
-
-    output:
-    tuple val(meta), path('*.gripss.filtered{,.somatic}.vcf.gz'), path('*.gripss.filtered{,.somatic}.vcf.gz.tbi'), emit: vcf
-    tuple val(meta), path('*.gripss{,.somatic}.vcf.gz'), path('*.gripss{,.somatic}.vcf.gz.tbi')                  , emit: vcf_unfiltered
-    path 'versions.yml'                                                                                          , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-
-    def reference_arg = meta.containsKey('normal_id') ? "-reference ${meta.normal_id}" : ''
-    def target_regions_bed_arg = target_region_bed ? "-target_regions_bed ${target_region_bed}" : ''
-    def output_id_arg = meta.containsKey('normal_id') ? '-output_id somatic' : ''
-
-    """
-    gripss \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
-        ${args} \\
-        -sample ${meta.tumor_id} \\
-        ${reference_arg} \\
-        -vcf ${gridss_vcf} \\
-        -ref_genome ${genome_fasta} \\
-        -ref_genome_version ${genome_ver} \\
-        -pon_sgl_file ${pon_breakends} \\
-        -pon_sv_file ${pon_breakpoints} \\
-        -known_hotspot_file ${known_fusions} \\
-        -repeat_mask_file ${repeatmasker_annotations} \\
-        ${target_regions_bed_arg} \\
-        ${output_id_arg} \\
-        -output_dir ./
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        gripss: \$(gripss -version | sed 's/^.* //')
-    END_VERSIONS
-    """
-
-    stub:
-    """
-    touch ${meta.tumor_id}.gripss.filtered.somatic.vcf.gz
-    touch ${meta.tumor_id}.gripss.filtered.somatic.vcf.gz.tbi
-    touch ${meta.tumor_id}.gripss.somatic.vcf.gz
-    touch ${meta.tumor_id}.gripss.somatic.vcf.gz.tbi
-    echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
-    """
-}
diff --git a/modules/local/gripss/somatic/meta.yml b/modules/local/gripss/somatic/meta.yml
deleted file mode 100644
index 060ed5cc..00000000
--- a/modules/local/gripss/somatic/meta.yml
+++ /dev/null
@@ -1,71 +0,0 @@
-name: gripss_somatic
-description: Filter and process GRIDSS somatic structural variants
-keywords:
-  - sv
-  - filtering
-  - somatic
-tools:
-  - gripss:
-      description: Apply filtering and post-processing to GRIDSS structural variants.
-      homepage: https://github.com/hartwigmedical/hmftools/tree/master/gripss
-      documentation: https://github.com/hartwigmedical/hmftools/tree/master/gripss
-      licence: ["GPL v3"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [id: 'sample_id', tumor_id: 'tumor_name', normal_id: 'normal_name']
-  - gridss_vcf:
-      type: file
-      description: VCF file
-      pattern: "*.{vcf.gz}"
-  - genome_fasta:
-      type: file
-      description: Reference genome assembly FASTA file
-      pattern: "*.{fa,fasta}"
-  - genome_ver:
-      type: string
-      description: Reference genome version
-  - genome_fai:
-      type: file
-      description: Reference genome assembly fai file
-      pattern: "*.{fai}"
-  - pon_breakend:
-      type: file
-      description: GRIDSS breakend PON file
-      pattern: "*.{bed.gz}"
-  - pon_breakpoints:
-      type: file
-      description: GRIDSS breakpoint PON file
-      pattern: "*.{bedpe.gz}"
-  - known_fusions:
-      type: file
-      description: HMF Known Fusions file
-      pattern: "*.{bedpe}"
-  - repeatmasker_annotations:
-      type: file
-      description: RepeatMasker annotations file
-  - target_region_bed:
-      type: file
-      description: Target region BED file (optional)
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [id: 'sample_id', tumor_id: 'tumor_name', normal_id: 'normal_name']
-  - vcf:
-      type: list
-      description: Hard filtered VCF file and index file
-      pattern: "*.{vcf.gz,vcf.gz.tbi}"
-  - vcf_unfiltered:
-      type: list
-      description: Unfiltered VCF file and index file
-      pattern: "*.{vcf.gz,vcf.gz.tbi}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@scwatts"

From 993bcb9175a3cfb12d4cbcbf137fa426cc101978 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 4 Jun 2025 15:51:19 +1000
Subject: [PATCH 78/88] update changelog

---
 CHANGELOG.md | 30 ++++++++++++++++++++++--------
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index dbfbe71a..2873957c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,19 +15,32 @@ Initial release of umccr/sash, created with the [nf-core](https://nf-co.re/) tem
 
 ### `Deprecated`
 
-## [0.6.0] – 2025-05-19
+## [0.6.0] - 2025-06-04
 
 ### Added
 
-- _none_
+- Software versions are now in `pipeline_info/software_versions.yml`
 
 ### Changed
 
-- SV caller switched GRIPSS → eSVe
-- Cancer-report Structural Variants plot: `SR`→`SF`, `PR`→`DF`
-- Linx upgraded 1.25 → 2.0
-- Purple upgraded 4.0.1 → 4.1.0
-- Bolt & GPGR updated for the adpat to above change
+- **SV caller:** GRIPSS → eSVee
+  - SV counts (unmelted & melted)
+  - CNV counts
+  - TMB-SV counts
+  - CopyNumberSegment counts
+  - SV in Circos plots
+  - Breakpoints & Breakends tables
+  - Copy-number variants tables
+  - Genome-wide somatic CNV segment tracks
+  - SV Map visualisation
+- Cancer-report Structural Variants summary plot:
+  - SR (Split Read) → SF (Split Fragments)
+  - PR (Paired-Read) → DF (Discordant Fragments)
+- Linx v1.25 → v2.0 (affects all Linx reports/files)
+- Purple v4.0.1 → v4.1.0
+  - MSI calculation relay on SAGE-specific tags #7
+  - (reverted) Circos have link sizes dependent on the size of SV #6
+- Filter PoN SV in cancer report tables #8
 
 ### Removed
 
@@ -38,10 +51,11 @@ Initial release of umccr/sash, created with the [nf-core](https://nf-co.re/) tem
 ### Deprecated
 
 - Metric aliases `SR`, `PR`
+- GRIDSS/GRIPSS modules
 
 ### Fixed
 
-- _none_
+- Nextflow `Stub` run
 
 ### Security
 

From 968f7a4905c3332e7bebe99340339b99f22fddff Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 6 Jun 2025 11:03:59 +1000
Subject: [PATCH 79/88] upgrade bolt container to ghcr.io/umccr/bolt:0.2.14-dev

---
 modules/local/bolt/other/multiqc_report/main.nf  | 2 +-
 modules/local/bolt/other/purple_baf_plot/main.nf | 2 +-
 modules/local/bolt/smlv_germline/prepare/main.nf | 2 +-
 modules/local/bolt/smlv_germline/report/main.nf  | 2 +-
 modules/local/bolt/smlv_somatic/annotate/main.nf | 2 +-
 modules/local/bolt/smlv_somatic/filter/main.nf   | 2 +-
 modules/local/bolt/smlv_somatic/report/main.nf   | 2 +-
 modules/local/bolt/smlv_somatic/rescue/main.nf   | 2 +-
 modules/local/bolt/sv_somatic/annotate/main.nf   | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/local/bolt/other/multiqc_report/main.nf b/modules/local/bolt/other/multiqc_report/main.nf
index d35be097..b42a1453 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/scwatts/bolt:0.2.13-multiqc'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev-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 1e24d501..cb70c8e6 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/scwatts/bolt:0.2.13-circos'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev-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 be419948..8a0bae23 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/scwatts/bolt:0.2.13'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev'
 
     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 b454e5ae..e5706842 100644
--- a/modules/local/bolt/smlv_germline/report/main.nf
+++ b/modules/local/bolt/smlv_germline/report/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_GERMLINE_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/scwatts/bolt:0.2.13-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_unfiltered_vcf)
diff --git a/modules/local/bolt/smlv_somatic/annotate/main.nf b/modules/local/bolt/smlv_somatic/annotate/main.nf
index 5374b5ca..659a50fc 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/scwatts/bolt:0.2.13-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf)
diff --git a/modules/local/bolt/smlv_somatic/filter/main.nf b/modules/local/bolt/smlv_somatic/filter/main.nf
index 310dc4bf..0208eabe 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/scwatts/bolt:0.2.13'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev'
 
     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 c5bbf6b9..13fe7196 100644
--- a/modules/local/bolt/smlv_somatic/report/main.nf
+++ b/modules/local/bolt/smlv_somatic/report/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/scwatts/bolt:0.2.13-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_filters_vcf), path(smlv_dragen_vcf), path(purple_purity)
diff --git a/modules/local/bolt/smlv_somatic/rescue/main.nf b/modules/local/bolt/smlv_somatic/rescue/main.nf
index 57fea4a2..e8802fbe 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/scwatts/bolt:0.2.13'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev'
 
     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 6437a4c1..1819ab16 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/scwatts/bolt:0.2.13-snpeff'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev-snpeff'
 
     input:
     tuple val(meta), path(sv_vcf), path(cnv_tsv)

From de018ece94fd798691dc1940020230ab1047b3b1 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 6 Jun 2025 11:58:58 +1000
Subject: [PATCH 80/88] update containers

---
 modules/local/bolt/other/cancer_report/main.nf   | 2 +-
 modules/local/bolt/sv_somatic/prioritise/main.nf | 2 +-
 modules/local/esvee/call/main.nf                 | 2 +-
 modules/local/linx/germline/main.nf              | 2 +-
 modules/local/linx/somatic/main.nf               | 2 +-
 modules/local/linx/visualiser/main.nf            | 2 +-
 modules/local/linxreport/main.nf                 | 2 +-
 modules/local/pave/somatic/main.nf               | 2 +-
 modules/local/purple/main.nf                     | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index cb02bbc7..67da0c6c 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/bolt:0.2.13-gpgr-esvee-5'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev-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)
diff --git a/modules/local/bolt/sv_somatic/prioritise/main.nf b/modules/local/bolt/sv_somatic/prioritise/main.nf
index 0a59abe6..616a5043 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 'docker.io/qclayssen/bolt:oncoanalyser-v2-2'
+    container 'ghcr.io/umccr/bolt:0.2.14-dev'
 
     input:
     tuple val(meta), path(sv_vcf)
diff --git a/modules/local/esvee/call/main.nf b/modules/local/esvee/call/main.nf
index 1447e79c..17c276c6 100644
--- a/modules/local/esvee/call/main.nf
+++ b/modules/local/esvee/call/main.nf
@@ -2,7 +2,7 @@ process ESVEE_CALL {
     tag "${meta.id}"
     label 'process_high'
 
-    container 'docker.io/qclayssen/esvee:1.0.3'
+    container 'ghcr.io/umccr/esvee:1.0.3'
 
 
     input:
diff --git a/modules/local/linx/germline/main.nf b/modules/local/linx/germline/main.nf
index 88c8c56e..cd03217c 100644
--- a/modules/local/linx/germline/main.nf
+++ b/modules/local/linx/germline/main.nf
@@ -2,7 +2,7 @@ process LINX_GERMLINE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/hmftools-linx:2.0--1'
+    container 'ghcr.io/umccr/linx:2.0'
 
     input:
     tuple val(meta), path(sv_vcf)
diff --git a/modules/local/linx/somatic/main.nf b/modules/local/linx/somatic/main.nf
index e96e5d8e..268c782a 100644
--- a/modules/local/linx/somatic/main.nf
+++ b/modules/local/linx/somatic/main.nf
@@ -2,7 +2,7 @@ process LINX_SOMATIC {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'docker.io/qclayssen/hmftools-linx:2.0--1'
+    container 'ghcr.io/umccr/linx:2.0'
 
     input:
     tuple val(meta), path(purple_dir)
diff --git a/modules/local/linx/visualiser/main.nf b/modules/local/linx/visualiser/main.nf
index 8eb1ae96..93eea38d 100644
--- a/modules/local/linx/visualiser/main.nf
+++ b/modules/local/linx/visualiser/main.nf
@@ -2,7 +2,7 @@ process LINX_VISUALISER {
     tag "${meta.id}"
     label 'process_medium'
 
-    container 'docker.io/qclayssen/hmftools-linx:2.0--1'
+    container 'ghcr.io/umccr/linx:2.0'
 
     input:
     tuple val(meta), path(linx_annotation_dir)
diff --git a/modules/local/linxreport/main.nf b/modules/local/linxreport/main.nf
index 957407c1..c6b84eff 100644
--- a/modules/local/linxreport/main.nf
+++ b/modules/local/linxreport/main.nf
@@ -2,7 +2,7 @@ process LINXREPORT {
     tag "${meta.id}"
     label 'process_single'
 
-    container 'docker.io/qclayssen/r-linxreport:1.1.0--0'
+    container 'ghcr.io/umccr/linxreport:1.1.0'
 
     input:
     tuple val(meta), path(linx_annotation_dir), path(linx_visualiser_dir)
diff --git a/modules/local/pave/somatic/main.nf b/modules/local/pave/somatic/main.nf
index 0a7c7954..ba048ad2 100644
--- a/modules/local/pave/somatic/main.nf
+++ b/modules/local/pave/somatic/main.nf
@@ -2,7 +2,7 @@ process PAVE_SOMATIC {
     tag "${meta.id}"
     label 'process_medium'
 
-    container 'docker.io/qclayssen/hmftools-pave:1.7--hdfd78af_0'
+    container 'ghcr.io/umccr/pave:1.6'
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/local/purple/main.nf b/modules/local/purple/main.nf
index 29512207..9670aad7 100644
--- a/modules/local/purple/main.nf
+++ b/modules/local/purple/main.nf
@@ -2,7 +2,7 @@ process PURPLE {
     tag "${meta.id}"
     label 'process_medium'
 
-    container 'docker.io/qclayssen/purple:4.1.0--1'
+    container 'ghcr.io/umccr/purple:4.1.0'
 
     input:
     tuple val(meta), path(amber), path(cobalt), path(sv_tumor_vcf), path(sv_tumor_tbi), path(sv_normal_vcf), path(sv_normal_tbi), path(smlv_tumor_vcf), path(smlv_normal_vcf)

From e2623860d11e3e5f6d364e3e7b1cae9d87658b53 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Fri, 6 Jun 2025 14:15:49 +1000
Subject: [PATCH 81/88] fix container name

---
 modules/local/pave/somatic/main.nf | 2 +-
 modules/local/purple/main.nf       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/pave/somatic/main.nf b/modules/local/pave/somatic/main.nf
index ba048ad2..a1581081 100644
--- a/modules/local/pave/somatic/main.nf
+++ b/modules/local/pave/somatic/main.nf
@@ -2,7 +2,7 @@ process PAVE_SOMATIC {
     tag "${meta.id}"
     label 'process_medium'
 
-    container 'ghcr.io/umccr/pave:1.6'
+    container 'ghcr.io/umccr/pave:1.7'
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/local/purple/main.nf b/modules/local/purple/main.nf
index 9670aad7..d7dde6ba 100644
--- a/modules/local/purple/main.nf
+++ b/modules/local/purple/main.nf
@@ -2,7 +2,7 @@ process PURPLE {
     tag "${meta.id}"
     label 'process_medium'
 
-    container 'ghcr.io/umccr/purple:4.1.0'
+    container 'ghcr.io/umccr/purple:4.1'
 
     input:
     tuple val(meta), path(amber), path(cobalt), path(sv_tumor_vcf), path(sv_tumor_tbi), path(sv_normal_vcf), path(sv_normal_tbi), path(smlv_tumor_vcf), path(smlv_normal_vcf)

From 43b988a1946bfd0dc8b0531ae038bf4dac02e4d9 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 12 Jun 2025 11:41:46 +1000
Subject: [PATCH 82/88] bump version to v0.6.0dev in nextflow.config

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 7a5d9757..79c1f4fb 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -173,7 +173,7 @@ manifest {
     description     = """Cancer WGTS post-processing pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.6'
-    version         = '0.5.0'
+    version         = 'v0.6.0dev'
     doi             = ''
 }
 

From be3c8e60fd671367be2a147dd39167bb68547a01 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 18 Jun 2025 13:37:04 +1000
Subject: [PATCH 83/88] Change explicit linx process name as in OA

---
 subworkflows/local/linx_plotting.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/subworkflows/local/linx_plotting.nf b/subworkflows/local/linx_plotting.nf
index 66cd4eaa..180082b8 100644
--- a/subworkflows/local/linx_plotting.nf
+++ b/subworkflows/local/linx_plotting.nf
@@ -2,8 +2,8 @@
 // LINX plotting visualises clusters structural variants
 //
 
-include { LINXREPORT as REPORT          } from '../../modules/local/linxreport/main'
-include { LINX_VISUALISER as VISUALISER } from '../../modules/local/linx/visualiser/main'
+include { LINXREPORT } from '../../modules/local/linxreport/main'
+include { LINX_VISUALISER } from '../../modules/local/linx/visualiser/main'
 
 workflow LINX_PLOTTING {
     take:
@@ -32,7 +32,7 @@ workflow LINX_PLOTTING {
                 return [meta_linx, anno_dir]
             }
 
-        VISUALISER(
+        LINX_VISUALISER(
             ch_linx_visualiser_inputs,
             genome_version,
             ensembl_data_resources,
@@ -57,7 +57,7 @@ workflow LINX_PLOTTING {
                 return [meta_linxreport, anno_dir, plot_dir]
             }
 
-        REPORT(
+        LINXREPORT(
             ch_linxreport_inputs,
         )
 

From 50af35a8e675dd0de11bc2c00d9992f26555ccef Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 18 Jun 2025 14:54:54 +1000
Subject: [PATCH 84/88] change linx channel

---
 subworkflows/local/linx_plotting.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/linx_plotting.nf b/subworkflows/local/linx_plotting.nf
index 180082b8..1cc9dc01 100644
--- a/subworkflows/local/linx_plotting.nf
+++ b/subworkflows/local/linx_plotting.nf
@@ -38,9 +38,9 @@ workflow LINX_PLOTTING {
             ensembl_data_resources,
         )
 
-        ch_versions = ch_versions.mix(VISUALISER.out.versions)
+        ch_versions = ch_versions.mix(LINX_VISUALISER.out.versions)
 
-        ch_visualiser_out = WorkflowSash.restoreMeta(VISUALISER.out.plots, ch_inputs)
+        ch_visualiser_out = WorkflowSash.restoreMeta(LINX_VISUALISER.out.plots, ch_inputs)
 
         // Create inputs and create process-specific meta
         // channel: [ meta_linxreport, linx_annotation_dir, linx_plot_dir ]
@@ -61,7 +61,7 @@ workflow LINX_PLOTTING {
             ch_linxreport_inputs,
         )
 
-        ch_versions = ch_versions.mix(REPORT.out.versions)
+        ch_versions = ch_versions.mix(LINXREPORT.out.versions)
 
     emit:
         plot_dir = ch_visualiser_out // channel: [ meta, plot_dir ]

From e82075f837450406be195e9b1033d3f26391a521 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Wed, 18 Jun 2025 16:51:11 +1000
Subject: [PATCH 85/88] update linx config

---
 conf/modules.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index b729e3af..0dc483aa 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -175,7 +175,7 @@ process {
         ]
     }
 
-    withName: '.*:LINX_ANNOTATION:(?:GERMLINE|SOMATIC)|.*:LINX_PLOTTING:VISUALISER' {
+    withName: '.*:LINX_ANNOTATION:(?:GERMLINE|SOMATIC)|.*:LINX_PLOTTING:LINX_VISUALISER' {
         ext.jarPath = '/opt/linx/linx.jar'
     }
 
@@ -195,7 +195,7 @@ process {
         ]
     }
 
-    withName: '.*:LINX_PLOTTING:VISUALISER' {
+    withName: '.*:LINX_PLOTTING:LINX_VISUALISER' {
         ext.circosPath = '/opt/conda/bin/circos'
         publishDir = [
             path: { "${params.outdir}" },
@@ -204,7 +204,7 @@ process {
         ]
     }
 
-    withName: '.*:LINX_PLOTTING:REPORT' {
+    withName: '.*:LINX_PLOTTING:LINXREPORT' {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,

From 3c742b2765e22d3b46504ab1bc116f223652b14c Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 19 Jun 2025 16:17:06 +1000
Subject: [PATCH 86/88] Remove dev tag for full release

---
 modules/local/bolt/other/cancer_report/main.nf   | 2 +-
 modules/local/bolt/other/multiqc_report/main.nf  | 2 +-
 modules/local/bolt/other/purple_baf_plot/main.nf | 2 +-
 modules/local/bolt/smlv_germline/prepare/main.nf | 2 +-
 modules/local/bolt/smlv_germline/report/main.nf  | 2 +-
 modules/local/bolt/smlv_somatic/annotate/main.nf | 2 +-
 modules/local/bolt/smlv_somatic/filter/main.nf   | 2 +-
 modules/local/bolt/smlv_somatic/report/main.nf   | 2 +-
 modules/local/bolt/smlv_somatic/rescue/main.nf   | 2 +-
 modules/local/bolt/sv_somatic/annotate/main.nf   | 2 +-
 modules/local/bolt/sv_somatic/prioritise/main.nf | 2 +-
 nextflow.config                                  | 4 ++--
 12 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
index 67da0c6c..e54bc8f9 100644
--- a/modules/local/bolt/other/cancer_report/main.nf
+++ b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.14-dev-gpgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-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)
diff --git a/modules/local/bolt/other/multiqc_report/main.nf b/modules/local/bolt/other/multiqc_report/main.nf
index b42a1453..099ffed6 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:0.2.14-dev-multiqc'
+    container 'ghcr.io/umccr/bolt:0.2.14-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 cb70c8e6..03a676d1 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:0.2.14-dev-circos'
+    container 'ghcr.io/umccr/bolt:0.2.14-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 8a0bae23..e3292f23 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:0.2.14-dev'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     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 e5706842..181ea027 100644
--- a/modules/local/bolt/smlv_germline/report/main.nf
+++ b/modules/local/bolt/smlv_germline/report/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_GERMLINE_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.14-dev-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_unfiltered_vcf)
diff --git a/modules/local/bolt/smlv_somatic/annotate/main.nf b/modules/local/bolt/smlv_somatic/annotate/main.nf
index 659a50fc..db49ffc7 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:0.2.14-dev-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf)
diff --git a/modules/local/bolt/smlv_somatic/filter/main.nf b/modules/local/bolt/smlv_somatic/filter/main.nf
index 0208eabe..b31055b5 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:0.2.14-dev'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     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 13fe7196..77ea9043 100644
--- a/modules/local/bolt/smlv_somatic/report/main.nf
+++ b/modules/local/bolt/smlv_somatic/report/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.14-dev-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_filters_vcf), path(smlv_dragen_vcf), path(purple_purity)
diff --git a/modules/local/bolt/smlv_somatic/rescue/main.nf b/modules/local/bolt/smlv_somatic/rescue/main.nf
index e8802fbe..68c39ada 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:0.2.14-dev'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     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 1819ab16..67b31c1d 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:0.2.14-dev-snpeff'
+    container 'ghcr.io/umccr/bolt:0.2.14-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 616a5043..d820477a 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:0.2.14-dev'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     input:
     tuple val(meta), path(sv_vcf)
diff --git a/nextflow.config b/nextflow.config
index 79c1f4fb..b3e7e165 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -168,12 +168,12 @@ dag {
 
 manifest {
     name            = 'umccr/sash'
-    author          = """Stephen Watts"""
+    author          = """Stephen Watts, Quentin Clayssen"""
     homePage        = 'https://github.com/umccr/sash'
     description     = """Cancer WGTS post-processing pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.6'
-    version         = 'v0.6.0dev'
+    version         = 'v0.6.0'
     doi             = ''
 }
 

From 3a28165078b2702de249d3da1683a002fc55fb46 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 19 Jun 2025 16:53:03 +1000
Subject: [PATCH 87/88] Update version format for bumpversion compatibility

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index b3e7e165..fd3cb879 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -173,7 +173,7 @@ manifest {
     description     = """Cancer WGTS post-processing pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.6'
-    version         = 'v0.6.0'
+    version         = '0.5.0'
     doi             = ''
 }
 

From a4615a6d954588038143fd2eb329b45528ffeb93 Mon Sep 17 00:00:00 2001
From: qclayssen <quentin.clayssen@gmail.com>
Date: Thu, 19 Jun 2025 17:10:01 +1000
Subject: [PATCH 88/88] =?UTF-8?q?Bump=20version:=200.5.0=20=E2=86=92=200.6?=
 =?UTF-8?q?.0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.cfg | 2 +-
 nextflow.config  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 8a061254..4313c56b 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.0
+current_version = 0.6.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[a-z0-9+]+)
diff --git a/nextflow.config b/nextflow.config
index fd3cb879..9a5a41e6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -173,7 +173,7 @@ manifest {
     description     = """Cancer WGTS post-processing pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.6'
-    version         = '0.5.0'
+    version         = '0.6.0'
     doi             = ''
 }