Add LRSOMATICREPORT as the final pipeline step

.gitattributes

@@ -2,3 +2,4 @@
 *.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated
+assets/lrsomatic_report/** linguist-vendored

.nf-core.yml

@@ -9,6 +9,9 @@ lint:
     - .github/workflows/awsfulltest.yml
     - .github/CONTRIBUTING.md
   files_unchanged:
+    # Exempt: carries `assets/lrsomatic_report/** linguist-vendored`, which keeps the
+    # vendored tool source out of GitHub's language statistics
+    - .gitattributes
     - CODE_OF_CONDUCT.md
     - assets/nf-core-lrsomatic_logo_light.png
     - docs/images/nf-core-lrsomatic_logo_light.png

.pre-commit-config.yaml

@@ -15,6 +15,7 @@ repos:
               .*ro-crate-metadata.json$|
               modules/(?!local/).*|
               subworkflows/(?!local/).*|
+              assets/lrsomatic_report/.*|
               .*\.snap$
           )$
       - id: end-of-file-fixer
@@ -23,6 +24,7 @@ repos:
               .*ro-crate-metadata.json$|
               modules/(?!local/).*|
               subworkflows/(?!local/).*|
+              assets/lrsomatic_report/.*|
               .*\.snap$
           )$
   - repo: https://github.com/seqeralabs/nf-lint-pre-commit

.prettierignore

@@ -12,3 +12,5 @@ bin/
 ro-crate-metadata.json
 modules/nf-core/
 subworkflows/nf-core/
+# Vendored upstream tool source -- see assets/lrsomatic_report/VENDORED.md
+assets/lrsomatic_report/

CHANGELOG.md

@@ -5,12 +5,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.2.0dev
 
+### `Added`
+
+- [#176](https://github.com/IntGenomicsLab/lrsomatic/pull/176) - Added `LRSOMATICREPORT` as the final pipeline step: a self-contained per-sample HTML report covering small variants, structural variants, copy number and QC. Skip it with `--skip_report`; choose the gene panel selected on load with `--report_gene_panel` (@ljwharbers).
+- [#176](https://github.com/IntGenomicsLab/lrsomatic/pull/176) - Vendored the [lrsomatic_report](https://github.com/ljwharbers/lrsomatic_report) v1.3.2 tool source at `assets/lrsomatic_report`, so `nextflow run IntGenomicsLab/lrsomatic` ships it without a submodule checkout (@ljwharbers).
+- [#176](https://github.com/IntGenomicsLab/lrsomatic/pull/176) - Added a `solution_dirs` output to the WAKHAN module so its per-solution copy-number plots can be staged downstream (@ljwharbers).
+
 ### `Changed`
 
+- [#186](https://github.com/IntGenomicsLab/lrsomatic/pull/186) - Re-synced the vendored [lrsomatic_report](https://github.com/ljwharbers/lrsomatic_report) to v1.3.0, which adds tickbox dropdown filters on the categorical columns of both variant tables and turns the report's gene panel selector into checkboxes (@ljwharbers).
+- [#176](https://github.com/IntGenomicsLab/lrsomatic/pull/176) - Re-synced the vendored [lrsomatic_report](https://github.com/ljwharbers/lrsomatic_report) to v1.3.2: facet dropdown counts follow the active filters, opening a facet menu no longer resets the table's horizontal scroll, a flatter clinical theme, and inline code comments trimmed to one line (@ljwharbers).
+- [#186](https://github.com/IntGenomicsLab/lrsomatic/pull/186) - `--report_gene_panel` now takes a comma-separated list, so several panels can be applied at once: a variant or SV is kept if it hits any of them. Panel values are also validated at launch instead of failing inside the report task (@ljwharbers).
 - [#184](https://github.com/IntGenomicsLab/lrsomatic/pull/184) - Replaced the CHM13 Severus panel of normals with the merged 1000 Genomes + ASAP panel (@AmberVerhasselt).
 
 ### `Fixed`
 
+- [#186](https://github.com/IntGenomicsLab/lrsomatic/pull/186) - Stopped snapshotting the md5 of sample4's merged tumour BAM and its index in the `clair_only` nf-test: `samtools merge` gives the colliding `@PG` IDs of the two replicates a random hex suffix, so neither digest is reproducible. The alignment records are, and are now asserted with `bam().getReadsMD5()` instead (@ljwharbers).
 - [#182](https://github.com/IntGenomicsLab/lrsomatic/pull/182) - Added `--vcf` to the default `vep_args` so VEP writes VCF output rather than its default tab-delimited format (@AmberVerhasselt).
 
 ## v1.1.0 - [2026-04-28]

CITATIONS.md

@@ -50,6 +50,10 @@
 
   > Lin JH, Chen LC, Yu SC, Huang YT. LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants. Bioinformatics. 2022 Apr 28;38(9):2452-2455. doi: 10.1093/bioinformatics/btac126. PubMed PMID: 35253834; PubMed Central PMCID: PMC9048675.
 
+- [lrsomatic_report](https://github.com/ljwharbers/lrsomatic_report)
+
+  > Standalone R/Quarto reporting tool that renders the pipeline's final per-sample HTML report. https://github.com/ljwharbers/lrsomatic_report
+
 - [minimap2](https://pubmed.ncbi.nlm.nih.gov/29750242/)
 
   > Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: 10.1093/bioinformatics/bty191. PubMed PMID: 29750242; PubMed Central PMCID: PMC6137996.

README.md

@@ -104,7 +104,7 @@ IntGenomicsLab/lr_somatic was originally written by Luuk Harbers, Robert Forsyth
 
 ## Pipeline output
 
-This pipeline produces a series of different output files. The main output is an aligned and phased tumour bam file. This bam file can be used by any typical downstream tool that uses bam files as input. Furthermore, we have sample-specific QC outputs from `cramino` (fastq), `cramino` (bam), `mosdepth`, `samtools` (stats/flagstat/idxstats), and optionally `fibertools`. Finally, we have a `multiqc` report from that combines the output from `mosdepth` and `samtools` into one html report.
+This pipeline produces a series of different output files. The main output is an aligned and phased tumour bam file. This bam file can be used by any typical downstream tool that uses bam files as input. Furthermore, we have sample-specific QC outputs from `cramino` (fastq), `cramino` (bam), `mosdepth`, `samtools` (stats/flagstat/idxstats), and optionally `fibertools`. Finally, we have a `multiqc` report that combines the output from `mosdepth` and `samtools` into one HTML report, and a self-contained per-sample HTML report (`<sample>/report/<sample>_report.html`) covering small variants, structural variants, copy number and QC in one place — disable it with `--skip_report`.
 
 Besides QC and the aligned and phased bam file, we have output from (structural) variant and copy number callers, of which some are optional. The output from these variant callers can be found in their respective folders. For small and structural variant callers (`clairS`, `clairS-TO`, and `severus`) these will contain, among others, `vcf` files with called variants. For `ascat` these contain files with final copy number information and plots of the copy number profiles.
 
@@ -128,6 +128,7 @@ Example output directory structure:
 │    │   ├── germline
 │    │   ├── somatic
 │    │   ├── SVs
+│    ├── report
 │
 ├── Sample 2
 │    ├── ascat

assets/lrsomatic_report/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Luuk Harbers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

assets/lrsomatic_report/R/circos.R

@@ -0,0 +1,263 @@
+suppressPackageStartupMessages({
+  library(circlize)
+  library(data.table)
+})
+
+# Colour palettes — keep in sync with --circos-* in assets/styles/report.scss
+
+# SBS-6 SNV palette (SigProfiler/COSMIC standard, softened slightly toward report ink/paper)
+SNV_COLOURS = c(
+  "C>A" = "#2EBAED",
+  "C>G" = "#1b1e22",
+  "C>T" = "#b3402f",
+  "T>A" = "#c7c2b8",
+  "T>C" = "#ADCC54",
+  "T>G" = "#F0D0CE"
+)
+
+# SV colours — saturated, hue-matched to --sv-* table tokens
+SV_COLOURS = c(
+  INS = "#cf5b46",
+  DEL = "#2f6db3",
+  INV = "#c08a1e",
+  DUP = "#3f7d4e"
+)
+
+SV_YPOS = c(INS = 1.0, DEL = 0.66, INV = 0.33, DUP = 0.05)
+
+# CNV colours — tied to the report spine
+CNV_COLOURS = c(
+  major = "#b3402f",  # brick = "more"
+  minor = "#0d5c75",  # teal  = "less"
+  total = "#1b1e22"   # ink
+)
+
+# BND/translocation link colour
+BND_COLOUR = "#8a5fa3"
+
+# Classify SNV into 6 SBS categories (C/T-ref normalised)
+.classify_mut = function(ref, alt) {
+  comp = c(A = "T", T = "A", C = "G", G = "C")
+  ref = toupper(ref); alt = toupper(alt)
+  use_comp = !(ref %in% c("C", "T"))
+  norm_ref = ifelse(use_comp, comp[ref], ref)
+  norm_alt = ifelse(use_comp, comp[alt], alt)
+  paste0(norm_ref, ">", norm_alt)
+}
+
+# Draw a circos plot to output_path (SVG or PNG by extension)
+draw_circos = function(snv_data = NULL,
+                       sv_nontrans = NULL,
+                       sv_trans = NULL,
+                       cnv_data = NULL,
+                       cytobands,
+                       chrom_lengths,
+                       chromosomes,
+                       output_path) {
+
+  # Filter cytobands and lengths to displayed chromosomes
+  cyto_filt = cytobands[cytobands$chrom %in% chromosomes, ]
+  lens_filt  = chrom_lengths[names(chrom_lengths) %in% chromosomes]
+  lens_filt  = lens_filt[chromosomes[chromosomes %in% names(lens_filt)]]
+
+  # Prepare SNV data
+  if (!is.null(snv_data) && nrow(snv_data) > 0) {
+    snv = as.data.table(snv_data)[nchar(ref) == 1 & nchar(alt) == 1]
+    snv = snv[chrom %in% chromosomes]
+    snv[, mut_cat := .classify_mut(ref, alt)]
+    snv[, circos_col := SNV_COLOURS[mut_cat]]
+    snv[is.na(circos_col), circos_col := "#AAAAAA"]
+  } else {
+    snv = data.table(chrom = character(), pos = integer(),
+                     mut_cat = character(), circos_col = character())
+  }
+
+  # Prepare SV (non-BND) data
+  if (!is.null(sv_nontrans) && nrow(sv_nontrans) > 0) {
+    sv_nt = as.data.table(sv_nontrans)[chrom %in% chromosomes]
+  } else {
+    sv_nt = data.table(chrom = character(), pos = integer(), end = integer(),
+                       svtype = character(), circos_pos = numeric(), circos_col = character())
+  }
+
+  # Prepare translocation (BND) data
+  if (!is.null(sv_trans) && nrow(sv_trans) > 0) {
+    sv_tr = as.data.table(sv_trans)[chrom %in% chromosomes & chrom2 %in% chromosomes]
+  } else {
+    sv_tr = data.table(chrom = character(), pos = integer(),
+                       chrom2 = character(), pos2 = integer())
+  }
+
+  # Prepare CNV data
+  if (!is.null(cnv_data) && nrow(cnv_data) > 0) {
+    cnv = as.data.table(cnv_data)[chr %in% chromosomes]
+    cnv = cnv[order(chr, startpos)]
+  } else {
+    cnv = data.table(chr = character(), startpos = integer(), endpos = integer(),
+                     major_cn = numeric(), minor_cn = numeric(), total_cn = numeric())
+  }
+
+  # Open device
+  ext = tolower(tools::file_ext(output_path))
+  if (ext == "svg") {
+    svglite::svglite(output_path, width = 8, height = 8)
+  } else {
+    png(output_path, width = 2400, height = 2400, res = 300)
+  }
+
+  plot.new()
+  circos.clear()
+
+  n_chr = length(chromosomes)
+  gap_degrees = c(rep(1.5, n_chr - 1), 7)
+
+  # Single quiet track surface; colours match the report.scss border/surface tokens
+  track_bg     = "#fbfaf6"
+  track_border = "#e4e0d6"
+
+  circos.par(
+    "start.degree" = 90,
+    "gap.degree"   = gap_degrees,
+    "track.margin" = c(0.006, 0.006),
+    "cell.padding" = c(0, 0, 0, 0)
+  )
+
+  # Build cytobands list as expected by circos.initializeWithIdeogram
+  cyto_list = list(
+    df          = cyto_filt,
+    chromosome  = chromosomes[chromosomes %in% unique(cyto_filt$chrom)],
+    chr.len     = lens_filt
+  )
+
+  circos.initializeWithIdeogram(cyto_list$df,
+                                chromosome.index = cyto_list$chromosome,
+                                plotType         = c("ideogram", "labels"),
+                                labels.cex       = 0.8)
+
+  # Pre-compute jitter once so it varies per chromosome but stays reproducible
+  set.seed(42)
+
+  # ---- Track 1: SNV dots (coloured by mutation category) ------------------
+  circos.trackPlotRegion(
+    factors      = chromosomes,
+    ylim         = c(0, 1),
+    bg.border    = track_border,
+    bg.col       = track_bg,
+    track.height = 0.16,
+    panel.fun    = function(region, value, ...) {
+      chr = get.cell.meta.data("sector.index")
+      sub_snv = snv[chrom == chr]
+      if (nrow(sub_snv) == 0) return(invisible(NULL))
+      y_jitter = runif(nrow(sub_snv), 0.05, 0.95)
+      # Translucent so a dense cloud reads as a tint, not confetti.
+      circos.points(
+        x   = sub_snv$pos,
+        y   = y_jitter,
+        col = adjustcolor(sub_snv$circos_col, alpha.f = 0.65),
+        pch = 19,
+        cex = 0.18
+      )
+    }
+  )
+
+  # ---- Track 2: Non-BND SVs (DEL/DUP/INV/INS as horizontal segments) -----
+  circos.trackPlotRegion(
+    factors      = chromosomes,
+    ylim         = c(0, 1),
+    bg.border    = track_border,
+    bg.col       = track_bg,
+    track.height = 0.10,
+    panel.fun    = function(region, value, ...) {
+      chr = get.cell.meta.data("sector.index")
+      sub_sv = sv_nt[chrom == chr & !is.na(circos_pos)]
+      if (nrow(sub_sv) == 0) return(invisible(NULL))
+      for (i in seq_len(nrow(sub_sv))) {
+        x1 = sub_sv$pos[i]
+        x2 = if (!is.na(sub_sv$end[i]) && sub_sv$end[i] > x1) sub_sv$end[i] else x1 + 1L
+        circos.segments(
+          x0  = x1, x1  = x2,
+          y0  = sub_sv$circos_pos[i], y1 = sub_sv$circos_pos[i],
+          col = sub_sv$circos_col[i],
+          lwd = 2.5
+        )
+      }
+    }
+  )
+
+  # Y-axis labels for SV track
+  tryCatch(
+    circos.yaxis(
+      side              = "left",
+      at                = c(0.05, 0.33, 0.66, 1.0),
+      labels            = c("DUP", "INV", "DEL", "INS"),
+      track.index       = 3,
+      sector.index      = chromosomes[1],
+      labels.niceFacing = TRUE,
+      labels.cex        = 0.45
+    ),
+    error = function(e) NULL
+  )
+
+  # ---- Track 3: ASCAT copy-number -----------------------------------------
+  circos.trackPlotRegion(
+    factors      = chromosomes,
+    ylim         = c(0, 4),
+    bg.border    = track_border,
+    bg.col       = track_bg,
+    track.height = 0.18,
+    panel.fun    = function(region, value, ...) {
+      chr = get.cell.meta.data("sector.index")
+      sub_cnv = cnv[chr == get.cell.meta.data("sector.index")]
+      if (nrow(sub_cnv) == 0) return(invisible(NULL))
+
+      xmax = lens_filt[chr]
+      if (!is.na(xmax)) {
+        for (y_ref in c(1, 2, 3)) {
+          circos.lines(c(0, xmax), c(y_ref, y_ref),
+                       col = track_border, lwd = 0.4, lty = "dotted")
+        }
+      }
+
+      circos.yaxis(
+        side              = "left",
+        at                = c(0, 1, 2, 3, 4),
+        labels            = c("0", "1", "2", "3", "4+"),
+        sector.index      = chromosomes[1],
+        labels.niceFacing = TRUE,
+        labels.cex        = 0.40
+      )
+
+      for (i in seq_len(nrow(sub_cnv))) {
+        xl = sub_cnv$startpos[i]; xr = sub_cnv$endpos[i]
+        maj = sub_cnv$major_cn[i]
+        circos.rect(xl, maj + 0.02, xr, maj + 0.12,
+                    col = CNV_COLOURS["major"], border = CNV_COLOURS["major"], lwd = 0.05)
+        min_cn = sub_cnv$minor_cn[i]
+        circos.rect(xl, min_cn - 0.12, xr, min_cn - 0.02,
+                    col = CNV_COLOURS["minor"], border = CNV_COLOURS["minor"], lwd = 0.05)
+        tot = sub_cnv$total_cn[i]
+        circos.rect(xl, tot - 0.03, xr, tot + 0.03,
+                    col = CNV_COLOURS["total"], border = CNV_COLOURS["total"], lwd = 0.05)
+      }
+    }
+  )
+
+  # ---- Translocation links (BND): one arc per mate-collapsed rearrangement ----
+  if (nrow(sv_tr) > 0) {
+    for (i in seq_len(nrow(sv_tr))) {
+      tryCatch(
+        circos.link(
+          sector.index1 = sv_tr$chrom[i],  point1 = sv_tr$pos[i],
+          sector.index2 = sv_tr$chrom2[i], point2 = sv_tr$pos2[i],
+          col = adjustcolor(BND_COLOUR, alpha.f = 0.45),
+          lwd = 0.9
+        ),
+        error = function(e) NULL
+      )
+    }
+  }
+
+  circos.clear()
+  dev.off()
+  invisible(output_path)
+}