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Hotfix #115

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eb51d56
snap, version update
robert-a-forsyth Nov 28, 2025
b5938f2
prettier
robert-a-forsyth Nov 28, 2025
5b24d20
view
robert-a-forsyth Dec 2, 2025
19b15b4
view
robert-a-forsyth Dec 2, 2025
77ae92f
view
robert-a-forsyth Dec 2, 2025
ada3e8f
channel fix
robert-a-forsyth Dec 2, 2025
742f0ee
update ascat for pdf plotting
robert-a-forsyth Dec 4, 2025
feeee90
change var
robert-a-forsyth Dec 4, 2025
0e9e256
prettier and linting
robert-a-forsyth Dec 4, 2025
c2c0c15
views
robert-a-forsyth Dec 8, 2025
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2 changes: 1 addition & 1 deletion .nf-core.yml
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Expand Up @@ -39,4 +39,4 @@ template:
outdir: .
skip_features:
- fastqc
version: 1.0.0
version: 1.1.0dev
4 changes: 3 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,9 @@
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).

## v1.0.0dev - [date]
## v1.1.0 - [date]

## v1.0.0 - [28 Nov 2025]

Initial release of IntGenomicsLab/lrsomatic, created with the [nf-core](https://nf-co.re/) template.

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5 changes: 2 additions & 3 deletions README.md
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@@ -1,7 +1,7 @@
# IntGenomicsLab/lrsomatic

[![GitHub Actions CI Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/nf-test.yml)
[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![GitHub Actions Linting Status](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml/badge.svg)](https://github.com/IntGenomicsLab/lrsomatic/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
Expand Down Expand Up @@ -159,8 +159,7 @@ If you would like to contribute to this pipeline, please see the [contributing g

## Citations

<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
<!-- If you use IntGenomicsLab/lrsomatic for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
If you use IntGenomicsLab/lrsomatic for your analysis, please cite it using the following doi: [10.5281/zenodo.17751829](https://doi.org/10.5281/zenodo.17751829)

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

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2 changes: 1 addition & 1 deletion assets/multiqc_config.yml
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@@ -1,5 +1,5 @@
report_comment: >
This report has been generated by the <a href="https://github.com/IntGenomicsLab/lrsomatic/releases/tag/1.0.0" target="_blank">IntGenomicsLab/lrsomatic</a> analysis pipeline.
This report has been generated by the <a href="https://github.com/IntGenomicsLab/lrsomatic/tree/dev" target="_blank">IntGenomicsLab/lrsomatic</a> analysis pipeline.
report_section_order:
"IntGenomicsLab-lrsomatic-methods-description":
order: -1000
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3 changes: 2 additions & 1 deletion conf/modules.config
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Expand Up @@ -278,7 +278,8 @@ process {
"min_map_qual": params.ascat_min_map_qual,
"longread_bins": params.ascat_longread_bins,
"allele_counter_flags": params.ascat_allelecounter_flags,
"penalty": params.ascat_penalty
"penalty": params.ascat_penalty,
"pdf_plots": params.ascat_pdf_plots
] }
publishDir = [
path: { "${params.outdir}/${meta.id}/ascat" },
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11 changes: 6 additions & 5 deletions modules/nf-core/ascat/main.nf
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3 changes: 2 additions & 1 deletion nextflow.config
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Expand Up @@ -55,6 +55,7 @@ params {
ascat_penalty = 150
ascat_purity = null
ascat_longread_bins = 2000
ascat_pdf_plots = "False"
ascat_allelecounter_flags = "-f 0"
ascat_chroms = null // Only use if running on a subset of chromosomes (c(1:22, 'X', 'Y'))

Expand Down Expand Up @@ -344,7 +345,7 @@ manifest {
mainScript = 'main.nf'
defaultBranch = 'main'
nextflowVersion = '!>=25.04.0'
version = '1.0.0'
version = '1.1.0dev'
doi = ''
}

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20 changes: 10 additions & 10 deletions ro-crate-metadata.json
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16 changes: 12 additions & 4 deletions subworkflows/local/tumor_normal_happhase.nf
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Expand Up @@ -22,6 +22,8 @@ workflow TUMOR_NORMAL_HAPPHASE {
somatic_vep = Channel.empty()
germline_vep = Channel.empty()

mixed_bams.view()
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Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

Copilot uses AI. Check for mistakes.

// Branch input bams in normal and tumour
mixed_bams
.branch{ meta, bam, bai ->
Expand All @@ -39,7 +41,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
return [basecall_model, meta, file]
}
.set{downloaded_model_files}

downloaded_model_files.view()
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Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

Suggested change
downloaded_model_files.view()

Copilot uses AI. Check for mistakes.
mixed_bams.normal
.map{ meta, bam, bai ->
def basecall_model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? meta.basecall_model : meta.clair3_model
Expand All @@ -48,11 +50,12 @@ workflow TUMOR_NORMAL_HAPPHASE {
platform: meta.platform,
sex: meta.sex,
fiber: meta.fiber,
basecall_model: meta.basecall_model,
basecall_model: basecall_model,
clairS_model: meta.clairS_model]
return [ basecall_model, new_meta, bam, bai ]
}
.set { normal_bams_model }
normal_bams_model.view()
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Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

Copilot uses AI. Check for mistakes.

normal_bams_model
.combine(downloaded_model_files,by:0)
Expand All @@ -61,6 +64,7 @@ workflow TUMOR_NORMAL_HAPPHASE {
return [meta, bam, bai, model, platform]
}
.set{ normal_bams }
normal_bams.view()
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Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

Copilot uses AI. Check for mistakes.

// normal_bams -> meta: [id, paired_data, platform, sex, fiber, basecall_model]
// bam: list of concatenated aligned bams
Expand All @@ -73,16 +77,18 @@ workflow TUMOR_NORMAL_HAPPHASE {
// remove type from so that information can be merged easier later
mixed_bams.tumor
.map{ meta, bam, bai ->
def basecall_model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? meta.basecall_model : meta.clair3_model
def new_meta = [id: meta.id,
paired_data: meta.paired_data,
platform: meta.platform,
sex: meta.sex,
fiber: meta.fiber,
basecall_model: meta.basecall_model,
basecall_model: basecall_model,
clairS_model: meta.clairS_model]
return[new_meta, bam, bai]
}
.set{ tumor_bams }
tumor_bams.view()
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Debug view() statement should be removed before merging. This appears to be temporary debugging code left in the subworkflow.

Suggested change
tumor_bams.view()

Copilot uses AI. Check for mistakes.

// tumor_bams -> meta: [id, paired_data, platform, sex, fiber, basecall_model]
// bam: list of concatenated aligned bams
Expand Down Expand Up @@ -163,6 +169,9 @@ workflow TUMOR_NORMAL_HAPPHASE {

// Add phased vcf to tumour bams and type information
// mix with the normal bams
tumor_bams.view()
LONGPHASE_PHASE.out.vcf.view()
Comment on lines +172 to +173
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Debug view() statements should be removed before merging. These appear to be temporary debugging code left in the subworkflow.

Suggested change
tumor_bams.view()
LONGPHASE_PHASE.out.vcf.view()

Copilot uses AI. Check for mistakes.

tumor_bams
.join(LONGPHASE_PHASE.out.vcf)
.map { meta, bam, bai, vcf ->
Expand Down Expand Up @@ -246,7 +255,6 @@ workflow TUMOR_NORMAL_HAPPHASE {
.join(LONGPHASE_PHASE.out.vcf)
.join(LONGPHASE_PHASE.out.tbi)
.set{tumor_normal_severus}

// tumor_normal_severus -> meta: [id, paired_data, platform, sex, fiber, basecall_model]
// tumor_bam: haplotagged aligned bam for tumor
// tumor_bai: indexes for tumor bam files
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4 changes: 2 additions & 2 deletions tests/default.nf.test.snap
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Expand Up @@ -82,7 +82,7 @@
"wget": "1.21.4"
},
"Workflow": {
"IntGenomicsLab/lrsomatic": "v1.0.0"
"IntGenomicsLab/lrsomatic": "v1.1.0dev"
}
},
[
Expand Down Expand Up @@ -369,6 +369,6 @@
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-11-28T14:26:44.508445086"
"timestamp": "2025-11-28T16:07:44.541483428"
}
}
4 changes: 3 additions & 1 deletion workflows/lrsomatic.nf
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Expand Up @@ -580,11 +580,13 @@ workflow LRSOMATIC {
}
.join(SEVERUS.out.all_vcf)
.set { wakhan_input }

wakhan_input.view()
ch_fasta.view()
Comment on lines +583 to +584
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Debug view() statements should be removed before merging. These appear to be temporary debugging code left in the workflow and will clutter the execution logs with channel contents.

Suggested change
wakhan_input.view()
ch_fasta.view()

Copilot uses AI. Check for mistakes.
WAKHAN (
wakhan_input,
ch_fasta
)


ch_versions = ch_versions.mix(WAKHAN.out.versions)
}
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