Dev

.gitignore

@@ -9,3 +9,4 @@ testing*
 null/
 .nf-test
 .nf-test.log
+out/

.nf-core.yml

@@ -27,7 +27,7 @@ lint:
     - validation.summary.beforeText
     - validation.summary.afterText
   schema_params: false
-nf_core_version: 3.5.1
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   author: Jonas Demeulemeester
@@ -39,4 +39,4 @@ template:
   outdir: .
   skip_features:
     - fastqc
-  version: 1.0.0
+  version: 1.1.0dev

CHANGELOG.md

@@ -3,7 +3,34 @@
 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]
+## v1.1.0dev - [2026-04-10]
+
+### `Added`
+
+- [#152](https://github.com/IntGenomicsLab/lrsomatic/pull/152) - Integrated modkit module for long-read base modification detection and analysis.
+- [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Added DeepVariant and DeepSomatic modules for germline and somatic variant calling from long-read sequencing data.
+- [#147](https://github.com/IntGenomicsLab/lrsomatic/pull/147) - Implemented whatshap_stats module to generate phase block statistics and phasing quality metrics.
+- [#141](https://github.com/IntGenomicsLab/lrsomatic/pull/141) - Added output of phased variants in separate VCF files for improved downstream analysis.
+- [#143](https://github.com/IntGenomicsLab/lrsomatic/pull/143) - Added Severus min_support parameter.
+- [#145](https://github.com/IntGenomicsLab/lrsomatic/pull/145) - Integrated MultiQC and nanoplot for comprehensive QC reporting with long-read sequencing metrics.
+- [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Added GPU support for Clair3, DeepVariant, and fibertools
+- [#150](https://github.com/IntGenomicsLab/lrsomatic/pull/150) - Added Claude GitHub Actions workflows for automated code review and PR assistance.
+
+### `Changed`
+
+- [#137](https://github.com/IntGenomicsLab/lrsomatic/pull/137) - Bulk module versions update. Fixed some issues with Wakhan.
+- [#138](https://github.com/IntGenomicsLab/lrsomatic/pull/138) - Perform QC before merging replicates
+- [#152](https://github.com/IntGenomicsLab/lrsomatic/pull/152) - Updated container versions and dependencies for modkit and related tools.
+- [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Refactored variant calling workflow to support both DeepVariant and existing callers with improved configuration handling.
+- [#140](https://github.com/IntGenomicsLab/lrsomatic/pull/140) - Improved documentation with additional pipeline usage examples and configuration guidance.
+
+### `Fixed`
+
+- [#137](https://github.com/IntGenomicsLab/lrsomatic/pull/137) - Resolved Nextflow strict syntax compliance issues for compatibility with latest Nextflow versions.
+- [#118](https://github.com/IntGenomicsLab/lrsomatic/pull/118) - Updated nf-core template components to align with latest pipeline standards.
+- [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Corrected bcftools and vcfsplit operations for accurate variant filtering and merging.
+
+## v1.0.0 - [28 Nov 2025]
 
 Initial release of IntGenomicsLab/lrsomatic, created with the [nf-core](https://nf-co.re/) template.
 

CITATIONS.md

@@ -8,6 +8,10 @@
 
 > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
 
+## [LRSomatic](https://doi.org/10.64898/2026.02.26.707772)
+
+> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-Lucía Rocha Iraizós, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772
+
 ## Pipeline tools
 
 - [ASCAT](https://pubmed.ncbi.nlm.nih.gov/20837533/)
@@ -95,3 +99,9 @@
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
+
+## Resources
+
+- [ASAP Panel of Normals](https://www.biorxiv.org/content/10.64898/2026.03.15.711881v1)
+
+  > Olga M. Sigalova, Alexandra Pančíková, Julie De Man, Koen Theunis, Gert J. Hulselmans, Vasileios Konstantakos, Bram Stuyven, Anton De Brabandere, Jarne Geurts, Antonina Mikorska, Shinjini Mukherjee, Sara Abouelasrar Salama, Katy Vandereyken, Kristofer Davie, Lukas Mahieu, Charles H. Adler, Thomas G. Beach, Geidy E. Serrano, Thierry Voet, Jonas Demeulemeester, Stein Aerts. Modeling cis-regulatory variation in human brain enhancers across a large Parkinson’s Disease cohort bioRxiv 2026.03.15.711881; doi: https://doi.org/10.64898/2026.03.15.711881

README.md

@@ -1,11 +1,13 @@
 # IntGenomicsLab/lrsomatic
 
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/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.17751829-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.17751829)
+[![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/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -21,6 +23,8 @@ It can be run in both **matched tumour-normal** and **tumour-only mode**, offeri
 
 Developed using **Nextflow DSL2**, it offers high portability and scalability across diverse computing environments. By leveraging Docker or Singularity containers, installation is streamlined and results are highly reproducible. Each process runs in an isolated container, simplifying dependency management and updates. Where applicable, pipeline components are sourced from **nf-core/modules**, promoting reuse, interoperability, and consistency within the broader Nextflow and nf-core ecosystems.
 
+For more information on how to run the pipeline, you can also go [here](https://intgenomicslab.github.io/lrsomatic).
+
 ## Pipeline summary
 
 ![image](./assets/lrsomatic_1.0.png)
@@ -161,7 +165,13 @@ If you would like to contribute to this pipeline, please see the [contributing g
 
 ## Citations
 
-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)
+If you use `IntGenomicsLab/lrsomatic` for your analysis, please cite it using the following:
+
+> LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data
+>
+> Robert A. Forsyth*, Luuk Harbers*, Amber Verhasselt, Ana-Lucía Rocha Iraizós, Sidi Yang, Joris Vande Velde, Christopher Davies, Nischalan Pillay, Laurens Lambrechts, Jonas Demeulemeester
+>
+> bioRxiv 2026.02.26.707772; doi: https://doi.org/10.64898/2026.02.26.707772
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

assets/multiqc_config.yml

@@ -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

assets/schema_input.json

@@ -50,6 +50,14 @@
             },
             "clairS_model": {
                 "type": "string"
+            },
+            "tumor_replicate": {
+                "type": "integer",
+                "default": 1
+            },
+            "normal_replicate": {
+                "type": "integer",
+                "default": 1
             }
         },
         "required": ["sample", "bam_tumor", "platform", "sex", "fiber"]

conf/base.config

@@ -26,6 +26,26 @@ process {
     //        adding in your local modules too.
     // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+    withLabel:process_gpu_high {
+        ext.use_gpu = { params.use_gpu as boolean }
+        accelerator = { (params.use_gpu as boolean) ? 1 : null }
+        cpus   = { 8      * task.attempt }
+        memory = { 48.GB  * task.attempt }
+        time   = { 8.h   * task.attempt }
+    }
+    withLabel:process_gpu_very_high {
+        ext.use_gpu = { params.use_gpu as boolean }
+        accelerator = { (params.use_gpu as boolean) ? 1 : null }
+        cpus   = { 16     * task.attempt }
+        memory = { 96.GB  * task.attempt }
+        time   = { 10.h   * task.attempt }
+    }
+    withLabel:process_gpu_very_high_memory {
+        ext.use_gpu = { params.use_gpu as boolean }
+        accelerator = { (params.use_gpu as boolean) ? 1 : null }
+        cpus   = { 16     * task.attempt }
+        memory = { 128.GB * task.attempt }
+    }
     withLabel:process_single {
         cpus   = { 1                   }
         memory = { 6.GB   * task.attempt }
@@ -52,20 +72,19 @@ process {
         time   = { 16.h   * task.attempt }
     }
     withLabel:process_long {
-        time   = { 20.h   * task.attempt }
+        time   = { 24.h   * task.attempt }
     }
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }
+    withLabel:process_short {
+        time   = { 1.h }
+    }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
     }
     withLabel:error_retry {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withLabel: process_gpu {
-        ext.use_gpu = { workflow.profile.contains('gpu') }
-        accelerator = { workflow.profile.contains('gpu') ? 1 : null }
-    }
 }

conf/igenomes.config

@@ -16,6 +16,8 @@ params {
             genome_name     = "hg38"
             ascat_alleles   = "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/ascat/G1000_alleles_hg38.zip"
             ascat_loci      = "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/ascat/G1000_loci_hg38.zip"
+            ascat_loci_gc   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip"
+            ascat_loci_rt   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip"
             centromere_bed  = "https://raw.githubusercontent.com/KolmogorovLab/Wakhan/refs/heads/main/src/annotations/grch38.cen_coord.curated.bed"
             pon_file        = "https://raw.githubusercontent.com/KolmogorovLab/Severus/refs/heads/main/pon/PoN_1000G_hg38.tsv.gz"
             bed_file        = "https://raw.githubusercontent.com/KolmogorovLab/Severus/refs/heads/main/vntrs/human_GRCh38_no_alt_analysis_set.trf.bed"
@@ -31,6 +33,7 @@ params {
             genome_name     = "CHM13"
             ascat_alleles   = "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/ascat/G1000_alleles_CHM13.zip"
             ascat_loci      = "https://raw.githubusercontent.com/IntGenomicsLab/test-datasets/main/references/ascat/G1000_loci_CHM13.zip"
+            ascat_loci_gc   = "https://github.com/IntGenomicsLab/test-datasets/raw/refs/heads/main/references/ascat/GCcontent_SNPloci_CHM13.txt.zip"
             centromere_bed  = "https://raw.githubusercontent.com/KolmogorovLab/Wakhan/refs/heads/main/src/annotations/chm13v2_cen_coord.bed"
             pon_file        = "https://raw.githubusercontent.com/KolmogorovLab/Severus/refs/heads/main/pon/PoN_1000G_chm13.tsv.gz"
             bed_file        = "https://raw.githubusercontent.com/KolmogorovLab/Severus/refs/heads/main/vntrs/chm13.bed"
@@ -40,6 +43,7 @@ params {
             dbsnp           = "${params.igenomes_base}/Homo_sapiens/ClairSTO/CHM13/Annotation/ClairSTO-pon/final_dbsnp.vcf.gz"
             onekgenomes     = "${params.igenomes_base}/Homo_sapiens/ClairSTO/CHM13/Annotation/ClairSTO-pon/final_1kgenomes.vcf.gz"
             colors          = "${params.igenomes_base}/Homo_sapiens/ClairSTO/CHM13/Annotation/ClairSTO-pon/final_colors.vcf.gz"
+            asap            = "${params.igenomes_base}/Homo_sapiens/ClairSTO/CHM13/Annotation/ClairSTO-pon/WGS_CHM13_ASAP.vcf.gz"
         }
         'GRCm38' {
             fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"