Modkit

.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 +3,9 @@
 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]
+## v1.1.0dev - [date]
+
+## 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/)

README.md

@@ -1,11 +1,12 @@
 # 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.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/)
-[![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/)
@@ -23,6 +24,8 @@ Developed using **Nextflow DSL2**, it offers high portability and scalability ac
 
 ## Pipeline summary
 
+![image](./assets/lrsomatic_1.0.png)
+
 **1) Pre-processing:**
 
 a. Raw read QC ([`cramino`](https://github.com/wdecoster/cramino))
@@ -159,8 +162,13 @@ 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:
+
+> 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 }
@@ -64,8 +84,4 @@ process {
         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"