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fix: wire NanoPlot pre/post stats into MultiQC #181

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1bc9048
fix: wire NanoPlot pre/post stats into MultiQC
ljwharbers Aug 13, 2026
f23b9b5
test: update default snapshot for NanoPlot MultiQC entries
ljwharbers Aug 13, 2026
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7 changes: 7 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,13 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## Unreleased

### `Fixed`

- [#181](https://github.com/IntGenomicsLab/lrsomatic/pull/181) - NanoPlot pre- and post-alignment statistics now reach MultiQC. `ch_nanoplot_pre_txt` and `ch_nanoplot_post_txt` were declared empty and mixed into the MultiQC inputs, but never assigned from `NANOPLOT_PRE.out.txt` / `NANOPLOT_POST.out.txt`, so the NanoStat section was silently missing from every report (@ljwharbers).
- [#181](https://github.com/IntGenomicsLab/lrsomatic/pull/181) - `NANOPLOT_PRE` now includes the replicate in its output prefix, so samples with more than one replicate no longer collapse into a single MultiQC sample (@ljwharbers).

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

### `Added`
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4 changes: 4 additions & 0 deletions CITATIONS.md
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Expand Up @@ -66,6 +66,10 @@

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [NanoPlot](https://pubmed.ncbi.nlm.nih.gov/37171891/)

> De Coster W, Rademakers R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics. 2023 May 4;39(5):btad311. doi: 10.1093/bioinformatics/btad311. PubMed PMID: 37171891; PubMed Central PMCID: PMC10196664.

- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/)

> Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
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5 changes: 4 additions & 1 deletion conf/modules.config
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Expand Up @@ -61,7 +61,10 @@ process {
}

withName: '.*:NANOPLOT_PRE' {
ext.prefix = { "${meta.id}_${meta.type}_ubam" }
// NANOPLOT_PRE runs once per replicate, so the replicate has to be part of the
// prefix -- otherwise every replicate produces an identically named NanoStats.txt
// and MultiQC keeps only one of them.
ext.prefix = { "${meta.id}_${meta.type}_rep${meta.replicate}_ubam" }
publishDir = [
path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam_rep${meta.replicate}" },
mode: params.publish_dir_mode,
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38 changes: 20 additions & 18 deletions docs/output.md
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Expand Up @@ -182,8 +182,8 @@ QC outputs are placed under `tumor/` for all samples, and additionally under `no
│ │ │ ├── sample_tumor_aln_NanoStats.txt
│ │ │ ├── sample_tumor_aln_NanoPlot-report.html
│ │ ├── nanoplot_ubam_rep1
│ │ │ ├── sample_tumor_ubam_NanoStats.txt
│ │ │ ├── sample_tumor_ubam_NanoPlot-report.html
│ │ │ ├── sample_tumor_rep1_ubam_NanoStats.txt
│ │ │ ├── sample_tumor_rep1_ubam_NanoPlot-report.html
│ │ ├── samtools
│ │ │ ├── sample.flagstat
│ │ │ ├── sample.idxstats
Expand All @@ -195,22 +195,22 @@ QC outputs are placed under `tumor/` for all samples, and additionally under `no
│ │ ├── sample.blocklist.tsv
```

| File | Description |
| ------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------ |
| `cramino_aln/sample_{type}_cramino.txt` | cramino QC summary statistics for the aligned bam file |
| `cramino_ubam_rep1/sample_{type}_cramino.txt` | cramino QC summary statistics for the unaligned bam files |
| `fibertoolsrs/sample_qc.txt` | fibertools QC summary for the bam file |
| `mosdepth/sample.mosdepth.global.dist.txt` | a cumulative distribution indicating the proportion of total bases that were covered for at least a given coverage value |
| `mosdepth/sample.mosdepth.summary.txt` | overall summary file from mosdepth tool |
| `nanoplot_aln/sample_{type}_aln_NanoStats.txt` | NanoPlot summary statistics for the aligned BAM file |
| `nanoplot_aln/sample_{type}_aln_NanoPlot-report.html` | NanoPlot interactive HTML report for the aligned BAM file |
| `nanoplot_ubam_rep1/sample_{type}_ubam_NanoStats.txt` | NanoPlot summary statistics for the unaligned BAM file |
| `nanoplot_ubam_rep1/sample_{type}_ubam_NanoPlot-report.html` | NanoPlot interactive HTML report for the unaligned BAM file |
| `samtools/sample.flagstat` | a summary of the counts of different samtools flags |
| `samtools/sample.idxstats` | a summary of the number of mapped and unmapped reads |
| `samtools/sample.stats` | summary statistics from the bamfile |
| `whatshap_stats/sample.stats.tsv` | WhatsHap phasing statistics per chromosome including phase block N50 and switch error rates |
| `whatshap_stats/sample.blocklist.tsv` | list of all phase blocks with their genomic coordinates |
| File | Description |
| ----------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------ |
| `cramino_aln/sample_{type}_cramino.txt` | cramino QC summary statistics for the aligned bam file |
| `cramino_ubam_rep1/sample_{type}_cramino.txt` | cramino QC summary statistics for the unaligned bam files |
| `fibertoolsrs/sample_qc.txt` | fibertools QC summary for the bam file |
| `mosdepth/sample.mosdepth.global.dist.txt` | a cumulative distribution indicating the proportion of total bases that were covered for at least a given coverage value |
| `mosdepth/sample.mosdepth.summary.txt` | overall summary file from mosdepth tool |
| `nanoplot_aln/sample_{type}_aln_NanoStats.txt` | NanoPlot summary statistics for the aligned BAM file |
| `nanoplot_aln/sample_{type}_aln_NanoPlot-report.html` | NanoPlot interactive HTML report for the aligned BAM file |
| `nanoplot_ubam_rep1/sample_{type}_rep1_ubam_NanoStats.txt` | NanoPlot summary statistics for the unaligned BAM file |
| `nanoplot_ubam_rep1/sample_{type}_rep1_ubam_NanoPlot-report.html` | NanoPlot interactive HTML report for the unaligned BAM file |
| `samtools/sample.flagstat` | a summary of the counts of different samtools flags |
| `samtools/sample.idxstats` | a summary of the number of mapped and unmapped reads |
| `samtools/sample.stats` | summary statistics from the bamfile |
| `whatshap_stats/sample.stats.tsv` | WhatsHap phasing statistics per chromosome including phase block N50 and switch error rates |
| `whatshap_stats/sample.blocklist.tsv` | list of all phase blocks with their genomic coordinates |

</details>

Expand Down Expand Up @@ -536,8 +536,10 @@ Phased variant calls produced by Longphase. Present in all samples.
│ │ ├── multiqc_data.json
│ │ ├── multiqc_general_stats.txt
│ │ ├── multiqc_software_versions.txt
│ │ ├── multiqc_nanostat.txt
│ │ ├── multiqc_sources.txt
│ │ ├── multiqc.log
│ │ ├── nanostat_fasta_stats_table.txt
│ ├── multiqc_plots
│ │ ├── pdf
│ │ │ ├── mosdepth-coverage-per-contig-multi-cnt.pdf
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8 changes: 6 additions & 2 deletions workflows/lrsomatic.nf
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Expand Up @@ -261,13 +261,15 @@ workflow LRSOMATIC {
if (!params.skip_nanoplot) {

//
// MODULE: NANOPLOT_PRE (label: process_medium)
// MODULE: NANOPLOT_PRE (label: process_low)
// Input: CRAMINO_PRE.out.arrow -- [meta, arrow_file]
// Output: nanoplot HTML/txt reports
//

NANOPLOT_PRE(CRAMINO_PRE.out.arrow)

ch_nanoplot_pre_txt = NANOPLOT_PRE.out.txt

}

}
Expand Down Expand Up @@ -844,13 +846,15 @@ workflow LRSOMATIC {
if (!params.skip_nanoplot) {

//
// MODULE: NANOPLOT_POST (label: process_medium)
// MODULE: NANOPLOT_POST (label: process_low)
// Input: CRAMINO_POST.out.arrow -- [meta, arrow_file]
// Output: HTML/txt QC reports (post-alignment)
//

NANOPLOT_POST(CRAMINO_POST.out.arrow)

ch_nanoplot_post_txt = NANOPLOT_POST.out.txt

}


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