umccr · qclayssen · Dec 9, 2024 · Feb 20, 2025 · Feb 20, 2025 · Feb 21, 2025
diff --git 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/CHANGELOG.md b/CHANGELOG.md
@@ -14,3 +14,58 @@ Initial release of umccr/sash, created with the [nf-core](https://nf-co.re/) tem
 ### `Dependencies`
 
 ### `Deprecated`
+
+## [0.6.0] - 2025-06-04
+
+### Added
+
+- Software versions are now in `pipeline_info/software_versions.yml`
+
+### Changed
+
+- **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
+
+- Kataegis module
+- CHORD HRD metrics
+- MSI load and status from purple
+
+### Deprecated
+
+- Metric aliases `SR`, `PR`
+- GRIDSS/GRIPSS modules
+
+### Fixed
+
+- Nextflow `Stub` run
+
+### 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/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
@@ -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}" },
@@ -171,7 +167,15 @@ process {
         ]
     }
 
-    withName: '.*:LINX_ANNOTATION:(?:GERMLINE|SOMATIC)|.*:LINX_PLOTTING:VISUALISER' {
+    withName: 'ESVEE_CALL' {
+        publishDir = [
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/esvee/${filename}" }
+        ]
+    }
+
+    withName: '.*:LINX_ANNOTATION:(?:GERMLINE|SOMATIC)|.*:LINX_PLOTTING:LINX_VISUALISER' {
         ext.jarPath = '/opt/linx/linx.jar'
     }
 
@@ -191,7 +195,7 @@ process {
         ]
     }
 
-  withName: '.*:LINX_PLOTTING:VISUALISER' {
+    withName: '.*:LINX_PLOTTING:LINX_VISUALISER' {
         ext.circosPath = '/opt/conda/bin/circos'
         publishDir = [
             path: { "${params.outdir}" },
@@ -200,20 +204,12 @@ process {
         ]
     }
 
-    withName: '.*:LINX_PLOTTING:REPORT' {
+    withName: '.*:LINX_PLOTTING:LINXREPORT' {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/${filename}" },
         ]
     }
 
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-
 }
diff --git 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",
@@ -21,6 +16,15 @@
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "utils_nfcore_pipeline": {
+                        "branch": "master",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         }
     }

diff --git 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 '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)
@@ -60,6 +60,7 @@ process BOLT_OTHER_CANCER_REPORT {
     stub:
     """
     mkdir -p output/
+    touch output/cancer_report.stub
     touch ${meta.tumor_id}.cancer_report.html
     echo -e '${task.process}:\\n  stub: noversions\\n' > versions.yml
     """

diff --git 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-multiqc'
 
     input:
     tuple val(meta), path(input_files)
@@ -35,6 +35,7 @@ process BOLT_OTHER_MULTIQC_REPORT {
     stub:
     """
     mkdir -p multiqc_report/multiqc_data/
+    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/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-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
@@ -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'
 
     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
@@ -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-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
@@ -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-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
@@ -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'
 
     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
@@ -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-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_filters_vcf), path(smlv_dragen_vcf), path(purple_purity)
@@ -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

diff --git 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'
 
     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
@@ -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-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
@@ -2,7 +2,7 @@ process BOLT_SV_SOMATIC_PRIORITISE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/scwatts/bolt:0.2.13'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     input:
     tuple val(meta), path(sv_vcf)

diff --git a/modules/local/gripss/Dockerfile → modules/local/esvee/call/Dockerfile b/modules/local/gripss/Dockerfile → modules/local/esvee/call/Dockerfile
@@ -7,7 +7,7 @@ RUN \
     zlib && \
   micromamba clean --all --yes
 
-FROM quay.io/biocontainers/hmftools-gripss:2.4--hdfd78af_0
+FROM quay.io/biocontainers/hmftools-esvee:1.0.3--hdfd78af_0
 
 COPY --from=build /env/ /env/
 

diff --git a/modules/local/esvee/call/main.nf b/modules/local/esvee/call/main.nf
@@ -0,0 +1,79 @@
+process ESVEE_CALL {
+    tag "${meta.id}"
+    label 'process_high'
+
+    container 'ghcr.io/umccr/esvee:1.0.3'
+
+
+    input:
+    tuple val(meta), path(ref_depth_vcf), path(prep_dir)
+    path genome_fasta
+    val genome_ver
+    path pon_breakends
+    path pon_breakpoints
+    path known_fusions
+    path repeatmasker_annotations
+
+    output:
+    tuple val(meta), path("caller/")                                                                                                     , emit: caller_dir
+    tuple val(meta), path("caller/${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
+    """
+}