added changelog and docs

.nf-core.yml

@@ -30,7 +30,7 @@ lint:
 nf_core_version: 3.5.2
 repository_type: pipeline
 template:
-  author: Jonas Demeulemeester
+  author: Robert Forsyth & Luuk Harbers
   description: Workflow for somatic variant calling of long read data
   force: false
   is_nfcore: false
@@ -39,4 +39,4 @@ template:
   outdir: .
   skip_features:
     - fastqc
-  version: 1.1.0dev
+  version: 1.1.0

CHANGELOG.md

@@ -3,32 +3,40 @@
 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).
 
-## v1.1.0dev - [2026-04-10]
+## v1.1.0 - [2026-04-28]
 
 ### `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.
+- [#117](https://github.com/IntGenomicsLab/lrsomatic/pull/117) - Added ASCAT PDF plots to output (@robert-a-forsyth).
+- [#126](https://github.com/IntGenomicsLab/lrsomatic/pull/126) - Added ASCAT raw segments txt files to output (@AmberVerhasselt).
+- [#135](https://github.com/IntGenomicsLab/lrsomatic/pull/135) - Added `skip_m6a` parameter to allow skipping m6A base modification steps (@robert-a-forsyth).
+- [#141](https://github.com/IntGenomicsLab/lrsomatic/pull/141) - Added output of phased variants in separate VCF files for improved downstream analysis (@ljwharbers).
+- [#143](https://github.com/IntGenomicsLab/lrsomatic/pull/143) - Added Severus `min_support` parameter and `skip_fibernormal` option (@ljwharbers).
+- [#145](https://github.com/IntGenomicsLab/lrsomatic/pull/145) - Integrated MultiQC and nanoplot for comprehensive QC reporting with long-read sequencing metrics (@ljwharbers).
+- [#147](https://github.com/IntGenomicsLab/lrsomatic/pull/147) - Implemented whatshap_stats module to generate phase block statistics and phasing quality metrics (@ljwharbers).
+- [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Added DeepVariant and DeepSomatic modules for germline and somatic variant calling from long-read sequencing data (@robert-a-forsyth).
+- [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Added GPU support for Clair3, DeepVariant, and fibertools (@robert-a-forsyth).
+- [#150](https://github.com/IntGenomicsLab/lrsomatic/pull/150) - Added Claude GitHub Actions workflows for automated code review and PR assistance (@ljwharbers).
+- [#152](https://github.com/IntGenomicsLab/lrsomatic/pull/152) - Integrated modkit module for long-read base modification detection and analysis (@robert-a-forsyth).
 
 ### `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.
+- [#123](https://github.com/IntGenomicsLab/lrsomatic/pull/123) - Updated channel structure (@robert-a-forsyth).
+- [#137](https://github.com/IntGenomicsLab/lrsomatic/pull/137) - Bulk module versions update. Fixed some issues with Wakhan (@ljwharbers).
+- [#138](https://github.com/IntGenomicsLab/lrsomatic/pull/138) - Perform QC before merging replicates (@robert-a-forsyth).
+- [#140](https://github.com/IntGenomicsLab/lrsomatic/pull/140) - Improved documentation with additional pipeline usage examples and configuration guidance (@ljwharbers).
+- [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Refactored variant calling workflow to support both DeepVariant and existing callers with improved configuration handling (@robert-a-forsyth).
+- [#152](https://github.com/IntGenomicsLab/lrsomatic/pull/152) - Updated container versions and dependencies for modkit and related tools (@robert-a-forsyth).
+- [#157](https://github.com/IntGenomicsLab/lrsomatic/pull/157) - Added ASAP Panel of Normals citation to CITATIONS.md (@ljwharbers).
+- [#160](https://github.com/IntGenomicsLab/lrsomatic/pull/160) - DeepVariant/DeepSomatic optimization and Panel-of-Normals handling improvements; updated docs; removed Claude workflow files (@robert-a-forsyth).
 
 ### `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.
+- [#116](https://github.com/IntGenomicsLab/lrsomatic/pull/116) - Corrected ASCAT GC and RT bias correction (@AmberVerhasselt).
+- [#118](https://github.com/IntGenomicsLab/lrsomatic/pull/118) - Updated nf-core template components to align with latest pipeline standards (@ljwharbers).
+- [#130](https://github.com/IntGenomicsLab/lrsomatic/pull/130) - Fixed path pattern for rephased VCF files (@Tim-Yu).
+- [#137](https://github.com/IntGenomicsLab/lrsomatic/pull/137) - Resolved Nextflow strict syntax compliance issues for compatibility with latest Nextflow versions (@ljwharbers).
+- [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Corrected bcftools and vcfsplit operations for accurate variant filtering and merging (@robert-a-forsyth).
 
 ## v1.0.0 - [28 Nov 2025]
 

modules/local/wakhan/main.nf

@@ -4,8 +4,8 @@ process WAKHAN {
 
     conda "${moduleDir}/environment.yml"
      container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://robertaforsyth/wakhan:0.4.2_iss58':
-        'robertaforsyth/wakhan:0.4.2_iss58' }"
+        'robertaforsyth/wakhan:0.4.2_iss58':
+        'docker://robertaforsyth/wakhan:0.4.2_iss58' }"
 
     input:
     tuple val(meta), path(tumor_input), path(tumor_index), path(normal_input), path(normal_index), path(vcf), path(breakpoints)

nextflow.config

@@ -381,7 +381,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.04.0'
-    version         = '1.1.0dev'
+    version         = '1.1.0'
     doi             = ''
 }