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

.gitignore

@@ -11,4 +11,4 @@ null/
 .nf-test/
 .nf-test.log
 CLAUDE.local.md
-.claude/
+.claude/

.nf-core.yml

@@ -9,6 +9,10 @@ lint:
     - .github/workflows/awsfulltest.yml
     - .github/CONTRIBUTING.md
   files_unchanged:
+    # Carries `assets/lrsomatic_report/** linguist-vendored` so the vendored tool
+    # source (see assets/lrsomatic_report/VENDORED.md) is excluded from GitHub's
+    # language statistics -- 338 KB of it is a single base64-font SCSS file.
+    - .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

@@ -5,6 +5,12 @@ 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) v1.1.0 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).
+
 ### `Fixed`
 
 - [#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).

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.

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 +1,266 @@
+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 and write it to output_path (SVG or PNG depending on extension)
+#
+# @param snv_data      data.table: chrom, pos, ref, alt  (single-base SNVs only)
+# @param sv_nontrans   data.table from parse_severus_vcf()$nontrans
+# @param sv_trans      data.table from parse_severus_vcf()$translocations
+# @param cnv_data      data.table from parse_ascat_segments()
+# @param cytobands     data.frame: chrom, start, end, name, stain
+# @param chrom_lengths named integer vector (chrom → bp length)
+# @param chromosomes   character vector of chroms to plot
+# @param output_path   path to the output file
+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, n_chr - 1), 5)
+
+  circos.par(
+    "start.degree" = 90,
+    "gap.degree"   = gap_degrees,
+    "track.margin" = c(0.008, 0.008),
+    "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,
+                                labels.cex       = 0.7)
+
+  # 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    = "#d8d3c8",
+    bg.col       = rep(c("#fcfbf7", "#f6f4ee"), length.out = n_chr),
+    track.height = 0.13,
+    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)
+      circos.points(
+        x   = sub_snv$pos,
+        y   = y_jitter,
+        col = sub_snv$circos_col,
+        pch = 19,
+        cex = 0.15
+      )
+    }
+  )
+
+  # ---- Track 2: Non-BND SVs (DEL/DUP/INV/INS as horizontal segments) -----
+  circos.trackPlotRegion(
+    factors      = chromosomes,
+    ylim         = c(0, 1),
+    bg.border    = "#d8d3c8",
+    bg.col       = rep(c("#f6f4ee", "#fcfbf7"), length.out = n_chr),
+    track.height = 0.11,
+    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$circos_col[i],
+          lwd = 2
+        )
+      }
+    }
+  )
+
+  # Y-axis labels for SV track
+  tryCatch(
+    circos.yaxis(
+      side              = "left",
+      at                = c(0.05, 0.33, 0.66, 1.0),
+      labels            = c("DUP", "INV", "DEL", "INS"),
+      track.index       = 3,
+      sector.index      = chromosomes[1],
+      labels.niceFacing = TRUE,
+      labels.cex        = 0.35
+    ),
+    error = function(e) NULL
+  )
+
+  # ---- Track 3: ASCAT copy-number -----------------------------------------
+  circos.trackPlotRegion(
+    factors      = chromosomes,
+    ylim         = c(0, 4),
+    bg.border    = "#d8d3c8",
+    bg.col       = rep(c("#fcfbf7", "#f6f4ee"), length.out = n_chr),
+    track.height = 0.17,
+    panel.fun    = function(region, value, ...) {
+      chr = get.cell.meta.data("sector.index")
+      sub_cnv = cnv[chr == get.cell.meta.data("sector.index")]
+      if (nrow(sub_cnv) == 0) return(invisible(NULL))
+
+      xmax = lens_filt[chr]
+      if (!is.na(xmax)) {
+        for (y_ref in c(1, 2, 3, 4)) {
+          circos.lines(c(0, xmax), c(y_ref, y_ref),
+                       col = "#d8d3c8", lwd = 0.3, lty = "dotted")
+        }
+      }
+
+      circos.yaxis(
+        side              = "left",
+        at                = c(0, 1, 2, 3, 4),
+        labels            = c("0", "1", "2", "3", "4+"),
+        sector.index      = chromosomes[1],
+        labels.niceFacing = TRUE,
+        labels.cex        = 0.30
+      )
+
+      for (i in seq_len(nrow(sub_cnv))) {
+        xl = sub_cnv$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) in the centre ----------------------------
+  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 = 0.5),
+          lwd = 0.8
+        ),
+        error = function(e) NULL
+      )
+    }
+  }
+
+  circos.clear()
+  dev.off()
+  invisible(output_path)
+}