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Merged
AmberVerhasselt merged 7 commits into from
Oct 2, 2026
Merged

Update Wakhan to 0.5.0 #214

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6467ebe
Update Wakhan to 0.5.0
ljwharbers Oct 1, 2026
4f1c7e1
Fill in PR number in CHANGELOG entry
ljwharbers Oct 1, 2026
786ef8e
Run lrsomatic_report 1.6.1
ljwharbers Oct 1, 2026
1ae5e77
Add a WAKHAN module stub test
ljwharbers Oct 1, 2026
2ee7d0a
Merge remote-tracking branch 'origin/chore/module-updates' into feat/…
ljwharbers Oct 1, 2026
9ff6d0c
Pull WAKHAN from Docker Hub, with the coverage-histogram fix
ljwharbers Oct 1, 2026
9edfb76
Merge origin/chore/module-updates (#213) into feat/wakhan-0.5.0
ljwharbers Oct 2, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -82,6 +82,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| `deepvariant` | 1.9.0 | 1.10.0 | nf-core update; `make_examples` now takes its flags from the model (`--checkpoint`): the ONT model is 199 wide with the new fuzzy channel, and both models call easy sites with the small model |
| `deepsomatic` | 1.7.0 | 1.10.0 | `make_examples_somatic` now takes its flags from the model (`--checkpoint`) instead of a hard-coded channel list and pileup width; the paired PacBio model is 147 wide with 9 channels. The small model is kept off explicitly (`--nocall_small_model_examples`), because the module does not pass its calls on |

- [#214](https://github.com/IntGenomicsLab/lrsomatic/pull/214) - Updated Wakhan from 0.4.4 to 0.5.0, run from `docker.io/ljwharbers/wakhan:0.5.0-histfix-1afd44d` (`oras://docker.io/ljwharbers/wakhan-sif:0.5.0-histfix-1afd44d` for Singularity/Apptainer) because no biocontainer was built for it. The image carries upstream commit 1afd44d4, which fixes the `IndexError` in `update_coverage_hist` that killed WAKHAN on some samples (KolmogorovLab/Wakhan#64). **The `wakhan/` output layout changes**: each solution is now `solution_{ploidy}_{purity}_{confidence}/` with `integer_profile.{bed,vcf,html,pdf}` (one boundary-aligned table for both haplotypes, replacing the two `*_HP_{1,2}.bed` files), `subclonal_profile.*`, `genes/genes_copynumber_states.*` and a `HiScanner_plots_data.zip` for the Wakhan web viewer; ranked solutions are `solution_rank_{n}`. Wakhan 0.5.0 no longer writes the per-chromosome `variation_plots`, `genome_copynumbers_details` plots or per-solution `loh_regions*.bed`. `LRSOMATICREPORT` now runs lrsomatic_report v1.6.1 (`ghcr.io/ljwharbers/lrsomatic-report:1.6.1`), which finds the copy-number plots in both layouts; v1.6.0 silently dropped them for 0.5.0 output. The WAKHAN stub now writes the outputs the module declares, and the version comes from `wakhan --version` (@ljwharbers).

## v1.1.0 - [2026-04-28]

### `Added`
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101 changes: 44 additions & 57 deletions docs/output.md
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Expand Up @@ -626,24 +626,28 @@ Mutational signature analysis of the PASS SNVs and indels in the phased somatic

```
├── wakhan
│ ├── {ploidy}_{purity}_{confidence}
│ │ ├── bed_output
│ ├── solution_{ploidy}_{purity}_{confidence}
│ │ ├── genes
│ │ │ ├── genes_copynumber_states.bed
│ │ │ ├── loh_regions.bed
│ │ │ ├── sample_{ploidy}_{purity}_{confidence}_HP_1.bed
│ │ │ ├── sample_{ploidy}_{purity}_{confidence}_HP_2.bed
│ │ ├── variation_plots
│ │ │ ├── chr{1-22,X,Y}_cn.html
│ │ │ ├── chr{1-22,X,Y}_cn.pdf
│ │ │ ├── CN_VARIATION_INDEX.html
│ │ ├── sample_{purity}_{ploidy}_{confidence}_genes_genome.html
│ │ ├── sample_{purity}_{ploidy}_{confidence}_genes_genome.pdf
│ │ ├── sample_{purity}_{ploidy}_{confidence}_genome_copynumbers_breakpoints.html
│ │ ├── sample_{purity}_{ploidy}_{confidence}_genome_copynumbers_breakpoints.pdf
│ │ ├── sample_{purity}_{ploidy}_{confidence}_genome_copynumbers_details.html
│ │ ├── sample_{purity}_{ploidy}_{confidence}_genome_copynumbers_details.pdf
│ │ │ ├── genes_copynumber_states.html
│ │ │ ├── genes_copynumber_states.pdf
│ │ ├── integer_profile.bed
│ │ ├── integer_profile.html
│ │ ├── integer_profile.pdf
│ │ ├── integer_profile.vcf
│ │ ├── subclonal_profile.bed
│ │ ├── subclonal_profile.html
│ │ ├── subclonal_profile.pdf
│ │ ├── subclonal_profile.vcf
│ │ ├── HiScanner_plots_data.zip
│ ├── solution_rank_{rank}
│ ├── coverage_data
│ │ ├── {0-23}_SNPS.csv
│ │ ├── {0-23}_SNPs.csv
│ │ ├── baf.csv
│ │ ├── cancer_genes_coverage.csv
│ │ ├── cn_coverage.png
│ │ ├── cn_peaks.png
│ │ ├── coverage.csv
│ │ ├── coverage_ps.csv
│ │ ├── phase_corrected_coverage.csv
│ │ ├── pileup_SNPs.csv
Expand All @@ -652,53 +656,36 @@ Mutational signature analysis of the PASS SNVs and indels in the phased somatic
│ │ ├── chr{1-22,X,Y}.pdf
│ │ ├── COVERAGE_INDEX.html
│ ├── phasing_output
│ │ ├── chr{1-22,X,Y}_phase_correction_0.html
│ │ ├── chr{1-22,X,Y}_phase_correction_1.html
│ │ ├── chr{1-22,X,Y}_phase_correction_{0.1,0.2,0.3,1,2}.html
│ │ ├── chr{1-22,X,Y}_without_phase_correction.html
│ │ ├── chr{1-22,X,Y}.pdf
│ │ ├── sample.rephased.vcf.gz
│ │ ├── sample.rephased.vcf.gz.tbi
│ │ ├── PHASE_CORRECTION_INDEX.html
│ │ ├── rephased.vcf.gz
│ │ ├── rephased.vcf.gz.csi
│ ├── snps_loh_plots
│ │ ├── chr{1-22,X,Y}_snps_loh.html
│ ├── sample_heatmap_ploidy_purity.html
│ ├── sample_heatmap_ploidy_purity.html.pdf
│ ├── sample_optimized_peak.html
│ │ ├── {sample}_genome_snps_ratio_loh.html
│ ├── {sample}_heatmap_ploidy_purity.html
│ ├── {sample}_heatmap_ploidy_purity.html.pdf
│ ├── solutions_ranks.tsv

```

| File | Description |
| ------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------- |
| `{ploidy}_{purity}_{confidence}/bed_output/genes_copynumber_states.bed` | bed file containing allele specific copy number values with coverage information |
| `{ploidy}_{purity}_{confidence}/bed_output/loh_regions.bed` | bed file containing positions of loss of heterozygosity regions |
| `{ploidy}_{purity}_{confidence}/bed_output/sample_{ploidy}_{purity}_{confidence}_HP_1.bed` | bed file containing copy number states, coverage, and SV breakpoints for haplotype 1 |
| `{ploidy}_{purity}_{confidence}/bed_output/sample_{ploidy}_{purity}_{confidence}_HP_2.bed` | bed file containing copy number states, coverage, and SV breakpoints for haplotype 2 |
| `{ploidy}_{purity}_{confidence}/variation_plots/chr{1-22,X,Y}_cn.html` | html based plotly plot of copy number and coverage for individual chromosomes |
| `{ploidy}_{purity}_{confidence}/variation_plots/chr{1-22,X,Y}_cn.pdf` | pdf based plotly plot of copy number and coverage for individual chromosomes |
| `{ploidy}_{purity}_{confidence}/variation_plots/CN_VARIATION_INDEX.html` | unclear html plot |
| `{ploidy}_{purity}_{confidence}/sample_{purity}_{ploidy}_{confidence}_genes_genome.html` | html plots of copy number variations in highlighted genes |
| `{ploidy}_{purity}_{confidence}/sample_{purity}_{ploidy}_{confidence}_genes_genome.pdf` | pdf plots of copy number variations in highlighted genes |
| `{ploidy}_{purity}_{confidence}/sample_{purity}_{ploidy}_{confidence}_genome_copynumbers_details.html` | genome-wide html copy number plots with coverage information on same axis |
| `{ploidy}_{purity}_{confidence}/sample_{purity}_{ploidy}_{confidence}_genome_copynumbers_details.pdf` | genome-wide pdf copy number plots with coverage information on same axis |
| `coverage_data/{0-23}_SNP.csv` | CSV of coverage data per chromosome |
| `coverage_data/coverage_ps.csv` | CSV of overall haplotype specific coverage data |
| `coverage_data/coverage.csv` | CSV of overall coverage data |
| `coverage_data/phase_corrected_coverage.csv` | CSV of overall phase-corrected coverage data |
| `coverage_data/pileup_SNPs.csv` | CSV of SNP pileup data |
| `coverage_plots/chr{1-22,X,Y}_cov.html` | chromosome specific html coverage plots |
| `coverage_plots/chr{1-22,X,Y}_cov.pdf` | chromosome specific pdf coverage plots |
| `coverage_plots/COVERAGE_INDEX.html` | unclear html plot |
| `phasing_output/chr{1-23,X,Y}_phase_correction_0.html` | Phase-switch error correction plot per chromosome |
| `phasing_output/chr{1-23,X,Y}_phase_correction_1.html` | Phase-switch error correction plot per chromosome |
| `phasing_output/chr{1-22,X,Y}_without_phase_correction.html` | Phase-switch error without phase correction plot per chromosome |
| `phasing_output/chr{1-22,X,Y}.pdf` | Phase-switch error correction plot |
| `phasing_output/sample_rephased.vcf.gz` | phase corrected SNP vcf file |
| `phasing_output/sample_rephased.vcf.gz.tbi` | phase corrected SNP vcf index file |
| `snps_loh_plots/chr{1-22,X,Y}_snps_loh.html` | interactive HTML plots of SNP allele frequencies and loss of heterozygosity regions per chromosome |
| `sample_heatmap_ploidy_purity.html` | heatmap html plot of purity ploidy fit |
| `sample_heatmap_ploidy_purity.html.pdf` | heatmap pdf plot of purity ploidy fit |
| `sample_optimized_peak.html` | optimization peak plot |
| `solutions_ranks.tsv` | rank of potential purity ploidy solutions |
| File | Description |
| ------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `solution_{ploidy}_{purity}_{confidence}/integer_profile.bed` | Integer copy-number segments for one purity/ploidy solution, both haplotypes on shared boundaries: coverage, copy-number state and confidence per haplotype, and the IDs of SV breakpoints in the segment |
| `solution_{ploidy}_{purity}_{confidence}/integer_profile.vcf` | The integer copy-number segments as VCF |
| `solution_{ploidy}_{purity}_{confidence}/integer_profile.html` | Interactive genome-wide plot of the integer copy-number profile with SV breakpoints (`.pdf`: static version) |
| `solution_{ploidy}_{purity}_{confidence}/subclonal_profile.*` | The same for subclonal copy-number states (`.bed`, `.vcf`, `.html`, `.pdf`) |
| `solution_{ploidy}_{purity}_{confidence}/genes/genes_copynumber_states.*` | Copy-number states of the genes of interest (`.bed`) and their plots (`.html`, `.pdf`) |
| `solution_{ploidy}_{purity}_{confidence}/HiScanner_plots_data.zip` | The solution's profiles, coverage, BAF and breakpoints bundled for the [Wakhan visualisation web viewer](https://wakhan-visualization.github.io/) |
| `solution_rank_{rank}` | The solution of that rank in `solutions_ranks.tsv` (a copy of its `solution_{ploidy}_{purity}_{confidence}` directory) |
| `coverage_data/*.csv` | Per-chromosome SNP tables, BAF, haplotype-specific and phase-corrected coverage, and SNP pileups; tumour-only runs also write `{sample}_loh_segments.csv` |
| `coverage_data/*.png` | Copy-number coverage and peak plots |
| `coverage_plots/chr{1-22,X,Y}_cov.html` | Coverage plot per chromosome (`.pdf`: static version); `COVERAGE_INDEX.html` links them |
| `phasing_output/*.html` | Phase-switch error plots per chromosome, with and without correction; `PHASE_CORRECTION_INDEX.html` links them |
| `phasing_output/rephased.vcf.gz` | Phase-corrected SNP VCF, with its `.csi` index |
| `snps_loh_plots/{sample}_genome_snps_ratio_loh.html` | SNP allele ratios and loss-of-heterozygosity regions (tumour-only runs) |
| `{sample}_heatmap_ploidy_purity.html` | Heatmap of the purity/ploidy fit (`.html.pdf`: static version) |
| `solutions_ranks.tsv` | Ranked purity/ploidy solutions; `repository_name` is the solution's directory |

</details>

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4 changes: 2 additions & 2 deletions modules/local/lrsomaticreport/main.nf
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Expand Up @@ -5,8 +5,8 @@ process LRSOMATICREPORT {
// No conda: the image ships render_report.R itself, not just its dependencies (guard in `script:`).
// TODO: switch to bioconda `lrsomatic-report` once the recipe in ljwharbers/lrsomatic_report is merged. Version bump = these two tags.
container "${(workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer') && !task.ext.singularity_pull_docker_container
? 'oras://ghcr.io/ljwharbers/lrsomatic-report-sif:1.6.0'
: 'ghcr.io/ljwharbers/lrsomatic-report:1.6.0'}"
? 'oras://ghcr.io/ljwharbers/lrsomatic-report-sif:1.6.1'
: 'ghcr.io/ljwharbers/lrsomatic-report:1.6.1'}"

input:
// Every path input is optional (`[]` when skipped); tumor/normal QC stage apart because a pair shares meta.id
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6 changes: 3 additions & 3 deletions modules/local/lrsomaticreport/tests/main.nf.test.snap
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Expand Up @@ -16,7 +16,7 @@
[
"LRSOMATICREPORT",
"lrsomatic_report",
"1.6.0"
"1.6.1"
]
],
"report": [
Expand All @@ -33,7 +33,7 @@
[
"LRSOMATICREPORT",
"lrsomatic_report",
"1.6.0"
"1.6.1"
]
]
}
Expand All @@ -50,7 +50,7 @@
[
"LRSOMATICREPORT",
"lrsomatic_report",
"1.6.0"
"1.6.1"
]
]
],
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2 changes: 1 addition & 1 deletion modules/local/wakhan/environment.yml
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Expand Up @@ -5,4 +5,4 @@ channels:
- bioconda
dependencies:
# renovate: datasource=conda depName=bioconda/wakhan
- bioconda::wakhan=0.4.4
- bioconda::wakhan=0.5.0
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