genomic-medicine-sweden/nallo: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

0.12.0dev - [XXXX-XX-XX]

Added

#921 - Added parameter --phased for GENMOD models if phasing is not skipped

Changed

#855 - Updated nf-core modules
#920 - Updated version to 0.12.0dev

Removed

Fixed

Parameters

Old parameter	New parameter

Note

Parameter has been updated if both old and new parameter information is present. Parameter has been added if just the new parameter information is present. Parameter has been removed if new parameter information isn't present.

Module updates

Tool	Old version	New version
modkit/bedmethyltobigwig	0.5.1-rc1	0.6.1
modkit/pileup	0.3.0	0.6.1
mosdepth	0.3.10	0.3.11
multiqc	1.31	1.33

Note

Version has been updated if both old and new version information is present. Version has been added if just the new version information is present. Version has been removed if new version information isn't present.

0.11.0 - [2026-03-04]

`Added`

#801 - Added Sentieon DNAscope long-read SNV calling with joint calling via Sentieon GVCFTyper
#801 - Added Dockerfile and build instructions for local module DNASCOPE_LONGREAD
#801 - Added configuration options for Sentieon model bundle paths, sequencing technology, and sex-specific BED intervals
#888 - Added parameters --create_maf_track, --create_hificnv_maf_track and --create_sawfish_maf_track
#888 - Added output of Sawfish visualization tracks
#890 - Added pre-commit hook to automatically generate parameters documentation
#899 - Added nf-core module bcftools/fixploidy for forcing diploid GTs in sentieon SNV calling
#902 - Added parameters for --edit, --fraction and --alpha options in STRDROP_CALL
#905 - Added subworkflow ANNOTATE_PARALOGS with Paraphrase JSON annotation by Paraphrase

`Changed`

#875 - Run Sawfish with --fast-cnv-mode in CI tests
#887 - Updated all pipeline testdata paths to same commit hash
#887 - Updated nf-test to trigger all tests on changes to samplesheet files that include pipeline testdata paths
#892 - Replaced local whatshap/haplotag module with nf-core module
#893 - Updated join to remove duplicate emissions for strict syntax
#894 - Updated nf-schema to 2.6.1 and minimum Nextflow version to 25.10.0 in order to run with strict syntax
#904 - Updated gens/preparecovandbaf to 1.1.5
#899 - Force diploid GTs for sentieon SNV calls
#909 - Changed Sawfish publishDir directive to strict syntax
#913 - Prep release 0.11.0
#917 - Updated paraphase to 3.5.0

`Removed`

#905 - Removed local module merge_json
#905 - Removed unused script bin/split_bed_chunks.py

`Fixed`

#908 - Unpublished VEP index that should not have been published

Parameters

Old parameter	New parameter
	`--extra_sawfish_options`
	`--sentieon_model_bundle`
	`--sentieon_tech`
	`--sentieon_male_haploid_bed`
	`--sentieon_male_diploid_bed`
	`--sentieon_female_diploid_bed`
	`--create_maf_track`
	`--create_hificnv_maf_track`
	`--create_sawfish_maf_track`
	`--strdrop_fraction`
	`--strdrop_alpha`
	`--strdrop_edit`

Note

Module updates

Tool	Old version	New version
gens/preparecovandbaf	1.1.4	1.1.5
sentieon/gvcftyper		202503.02
sentieon/dnascope-longread		1.5.2
merge_json_sample_files_into_family	1.0
paraphrase		0.2.0
paraphase	3.3.4	3.5.0
samtools (paraphase)	1.22.1	1.23

Note

0.10.2 - [2026-02-09]

`Changed`

#885 - Increased default memory requirements for PREPARE_GENS_INPUTS:GATK4_DENOISEREADCOUNTS

`Fixed`

#885 - Fixed non-contiguous chromosome blocks error in CONCAT_SORT_GENS:BCFTOOLS_CONCAT

0.10.1 - [2026-02-05]

`Changed`

#881 - Changed to separate inputs for female and male gens panel of normals

Parameters

Old parameter	New parameter
`--gens_panel_of_normals`	`--gens_panel_of_normals_female`
`--gens_panel_of_normals`	`--gens_panel_of_normals_male`

Note

0.10.0 - [2026-02-04]

`Added`

#807 - Added new workflow for generating input data (coverage and B-allele frequencies, BAF) to Gens.

`Changed`

#840 - Updated version to 0.10.0dev
#847 - Changed local whatshap/stats module to the nf-core module
#853 - Changed local whatshap/phase module to the nf-core module
#857 - Set SOMALIER_PED_FAMILY publishDir mode to match the rest of the pipeline processes
#866 - Updated test data and test snapshots
#870 - Fixed order of BAM files for whatshap phasing
#876 - Prep for release 0.10.0

`Removed`

#858 - Removed validation for empty samplesheet, because it obfuscates other errors

`Fixed`

#871 Fixed MethBat region validation running even when methylation calling is skipped

Parameters

Old parameter	New parameter
	`--skip_prepare_gens_input`
	`--gens_baf_positions`
	`--gens_panel_of_normals`
	`--gens_coverage_bins`

Note

Module updates

Tool	Old version	New version
gatk4/denoisereadcounts		4.6.2.0
gens/preparecovandbaf		1.4.0
cat/cat		2.8

Note

0.9.2 - [2026-01-27]

`Fixed`

#865 - Added check that methbat_regions parameter is set when running methbat

0.9.1 - [2026-01-05]

`Changed`

#848 - Updated genmod to 3.10.2 to avoid KeyErrors in genmod compound

Module updates

Tool	Old version	New version
genmod	3.10.1	3.10.2

Note

0.9.0 - [2025-12-19]

`Added`

#800 - Added co-phasing of SNVs and SVs for HiPhase and Longphase
#803 - Added new subworkflow CHROMOGRAPH to generate chromograph plots of autozygosity
#803 - Added new subworkflow VCF_CONCAT_SORT to concatenate and sort variants
#804 - Added sambamba depth to QC_ALIGNED_READS
#804 - Added separate region inputs for mosdepth and sambamba depth that both use --qc_regions as default
#819 - Added new CALL_METHYLATION_METHBAT subworkflow for methylation analysis of pacbio data
#824 - Added parameters for genmod compound penalty and threshold values
#831 - Added strdrop in a new ANNOTATE_REPEAT_EXPANSIONS subworkflow

`Changed`

#795 - Updated version to 0.9.0dev
#800 - Moved phasing subworkflow to run before annotation
#803 - Updated testdata and tests with gnomad allele frequencies in SNV annotation
#804 - Changed to only output d4-file from mosdepth when --mosdepth_d4_output is set, due to bugs in the d4-format
#813 - Updated nf-core template to 3.5.1
#819 - Renamed METHYLATION subworkflow to CALL_METHYLATION_MODKIT and changed output structure
#821 - Updated README to fix mistakes after template merge
#822 - Updated metromap and added .ai file
#826 - Updated HIPHASE tests because of unstable snapshots
#827 - Updated the chromograph implementation added in #803 to fix resume issues
#829 - Updated all Channel to channel
#830 - Updated implicit to explicit closure parameters
#831 - Updated stranger and moved it to ANNOTATE_REPEAT_EXPANSIONS
#832 - Updated citations and bibliography texts generation to work with topics channels
#838 - Updated github nf-test action to add cleanup for singularity tests that pull docker containers

`Removed`

#800 - Removed output of phased variants without annotation
#812 - Removed unnecessary flag vcf_stats_report in DEEPVARIANT_RUNDEEPVARIANT
#822 - Removed .svgz version of metromap

`Fixed`

#828 - Fixed no samples found in samplesheet error overriding actual errors

Parameters

Old parameter	New parameter
	`--skip_chromograph`
	`--bcftools_roh_af_tag`
	`--chromograph_af_tag`
	`--plot_chromograph_coverage`
	`--plot_chromograph_autozygosity`
	`--rhocallviz_af_tag`
	`--rhocallviz_min_af`
	`--rhocallviz_min_qual`
	`--tiddit_bin_size`
	`--genmod_compound_snv_penalty`
	`--genmod_compound_snv_threshold`
	`--genmod_compound_sv_penalty`
	`--genmod_compound_sv_threshold`
	`--genmod_compound_singleton_snv_penalty`
	`--genmod_compound_singleton_snv_threshold`
	`--genmod_compound_singleton_sv_penalty`
	`--genmod_compound_singleton_sv_threshold`
	`--genmod_compound_trio_snv_penalty`
	`--genmod_compound_trio_snv_threshold`
	`--genmod_compound_trio_sv_penalty`
	`--genmod_compound_trio_sv_threshold`
	`--mosdepth_d4_output`
	`--mosdepth_regions`
	`--sambamba_regions`
	`--skip_sambamba_depth`
`--methylation_call_regions`	`--modkit_call_regions`
`--skip_methylation_pileups`	`--skip_methylation_calling`
	`--methbat_male_label`
	`--methbat_female_label`
	`--run_methbat`
	`--run_modkit`
	`--extra_methbat_profile_options`
	`--methbat_regions`
	`--strdrop_training_set_json`

Note

Module updates

Tool	Old version	New version
chromograph		1.3.1
bcftools/concat	1.22	1.21
bcftools/roh		1.22
rhocall/viz		0.5.1
tiddit		3.9.3
methbat/profile		0.16.1
pbcpgtools/alignedbamtocpgscores		3.0.0
strdrop		0.3.1
stranger	0.9.5	0.10.0
trgt	4.0.0	5.0.0
modkit/bedmethyltobigwig	0.5.1-rc1	0.6.1
modkit/pileup	0.3.0	0.6.1
mosdepth	0.3.10	0.3.11
multiqc	1.31	1.33

Note

0.8.1 - [2025-10-31]

`Changed`

#796 - Updated SV-calling parameters description examples to include sawfish

`Fixed`

#796 - Fixed sorting of phase blocks GTF file (backported from 0.7.1)

0.8.0 - [2025-10-28]

`Added`

#654 - Added SPLIT_BED_CHUNKS to BEDTOOLS_SPLIT in the SCATTER_GENOME workflow
#671 - Added a test without --filter_variants_hgnc_ids
#691 - Added samplesheet validation requiring at least one sample, and require each row to be unique
#692 - Added the capability to run the pipeline in -stub mode
#705 - Add stub pipeline test for cadd_prescored_indels and cadd_resources with mock resources
#706 - Added a logo to README.md
#707 - Added a clean up step to the nf-test CI
#709 - Added nf-test for ANNOTATE_CADD
#713 - Added nfcore module yak/counts
#718 - Added a find-tests action to find all nf-tests to be run during CI
#726 - Added new parameters for finer-grained control over analysis regions
#727 - Added a stub test with mock uncompressed VEP cache
#736 - Added a new pre_vep_snv_filter_expression parameter in order to filter variants during the annotation
#737 - Added nf-test for PREPARE_REFERENCES
#738 - Added nf-test for QC_ALIGNED_READS
#739 - Added nf-test for CONVERT_INPUT_FILES
#740 - Added a check/early fail if trying to split the SNV calling into too many parallel processes
#743 - Added warnings about restrictive PacBio licenses, even when running a PacBio preset
#745 - Added relationships to sample meta
#745 - Added samplesheet validations for parents requiring known and correct sex
#746 - Added nf-test for GENOME_ASSEMBLY
#746 - Added samplesheet validation requiring unique sample names across all families
#746 - Added samplesheet validation requiring parents to exist in family
#748 - Added stub tests for skipping alignment and genome assembly
#758 - Added new QC_SNVS, GVCF_GLNEXUS_NORM_VARIANTS and VCF_CONCAT_NORM_VARIANTS subworkflows by splitting up CALL_SNVS
#766 - Added bigWig output to methylation subworkflow.
#768 - Added new SV caller Sawfish
#781 - Added a stub test where sample and family ID is the same

`Changed`

#654 - Changed SPLIT_BED_CHUNKS to BEDTOOLS_SPLIT in the SCATTER_GENOME workflow
#656 - Updated version to 0.7.0dev
#671 - Updated genmod to 3.10.1
#671 - Changed filtering from after ranking variants to between annotation and ranking. This ensures the correct most_severe_consequence and most_severe_pli are added to the filtered (clinical) and unfiltered (research) variants
#671 - Changed the unfiltered and filtered output files to _research and _clinical
#671 - Changed to publish all family level SVs from a single final process
#672 - Changed bcftools stats to run on unannotated variants instead of annotated (and ranked) variants
#672 - Changed the output directory of bcftools stats to qc/bcftools_stats
#672 - Changed the SNV outputs per sample to unannotated calls, matching the behavior of SVs
#677 - Changed echtvar_snv_databases from required to an optional parameter
#678 - Updated modules
#680 - Updated more modules
#685 - Updated patch for VEP missed in #680
#703 - Updated SNV_ANNOTATION test meta.id field to mitigate presumable bug in nf-test
#704 - Simplified HiPhase saveAs logic
#708 - Refactored repeat annotation
#707 - Updated DeepVariant to 1.9.0
#712 - Bump version to 0.8.0dev
#717 - Use family ID in RankScore repeat annotation
#718 - Updated nf-core template to v3.3.1
#721 - Updated samplesheet_multisample_bam with HG004 to complete a trio, and added a second family to samplesheet_multisample_ont_bam in order to perform more comprehensive testing
#723 - Refactored SV-calling for more flexiblity when choosing callers
#723 - Changed default SV-caller from Severus to Sniffles and HiFiCNV
#724 - Changed the inputs for the FASTQ conversion for the assembly subworkflow to use split BAM files instead of input BAM files when suitable
#726 - Changed cram output test from samplesheet_multisample_bam to samplesheet_target_regions_null (run on PR towards master), because of slow nf-test
#728 - Changed to only run CRAM conversion for unphased reads when not phasing reads, since they are not published when phasing
#732 - Updated logic associated with validateSVCallingParameters() to fix an issue added in #723
#733 - Reduced the disk space cleanup added to the CI in #707 to reduce the step time
#734 - Renamed subworkflows for more consistent naming
#746 - Renamed the ASSEMBLY subworkflow to GENOME_ASSEMBLY
#746 - Changed the default hifiasm strategy to trio-binning whenever parental reads are available
#748 - Improved pipeline test assertations and removed irrelevant pipeline tests from stub tests
#755 - Updated nf-core template to v3.3.2
#758 - Updated ADD_FOUND_IN_TAG to work with emtpy (.) INFO field
#758 - Updated (internal) per sample DeepVariant calls to include FOUND_IN tag
#760 - Updated the assembly documentation
#765 - Updated paraphase to 3.3.4
#768 - Changed hificnv_* parameters to cnv_* to reflect that they can be used for both HiFiCNV and Sawfish
#768 - Clarified PacBio software licence warning. Changed to only warn instead of error for --preset ONT_R10.
#774 - Changed local cramino module to nf-core cramino module
#779 - Changed to always run samtools merge, even if there is only one input file
#780 - Updated modkit/bedmethyltobigwig to release candidate version, otherwise crashing due to unsorted bed
#781 - Changed bcftools reheader prefix in SV-calling workflow to remedy a mistake introduced in #723
#784 - Updated metro map
#785 - Updated nf-core modules
#786 - Changed local subworflow filter_variants to nf-core vcf_filter_bcftools_ensemblvep
#786 - Changed samplesheet_multisample_bam test to include filter_snvs_expression and filter_svs_expression, and moved filter_variants_hgnc_ids = null to samplesheet_multisample_ont_bam
#787 - Updated more modules
#787 - Prep release 0.8.0
#789 - Updated parameters.md, removed autoformatting which brakes the document
#791 - Changed YAK_COUNT label back to process_high
#792 - Changed YAK_COUNT label back to process_high, correctly

`Removed`

#654 - Removed local module SPLIT_BED_CHUNKS
#672 - Removed BCFTOOLS_PLUGINSPLIT
#704 - Removed HiPhase stats, blocks and summary files and sorting of variants
#713 - Removed local yak module
#723 - Removed the CNV calling subworkflow
#723 - Removed sample-level SV outputs
#736 - Removed bcftools filltags from the SNV annotation subworkflow that added an AC entry
#741 - Removed bcftools filltags from the SNV calling subworkflow, that previosuly added an AC entry
#742 - Removed local module bcftools fillfromfasta that is no longer used in the pipeline
#756 - Removed unused components in subworkflows
#789 - Removed autoformatting from parameters docs which broke the document

`Fixed`

#671 - Fixed chrM/MT mismatches in the variant ranking (#499)
#718 - Fixed tests for add_found_in_tag, call_cnvs, create_pedigree_file, create_samples_haplotypes_file, filter_variants and scatter_genome that were not previously automatically tested in the CI.
#731 - Fixed invalid example samplesheet in README
#748 - Fixed improper } character appearing in aligned reads filename when phasing was disabled
#751 - Fixed linting issue in validatePacBioLicense
#756 - Fixed missing versions for ADD_FOUND_IN_TAG
#760 - Fixed the preset documentation not taking into account ONT assembly that was added in 0.5.0
#765 - Fixed missing samples/haplotypes in paraphase VCFs (#764)
#770 - Fixed broken link for GRCh38 PAR file in docs
#775 - Fixed docs for hifiasm_preset parameter
#779 - Fixed input files with fewer reads than --alignment_processes causing silent fails (#757)
#782 - Fixed null in SNV filename when running with --skip_snv_annotation --skip_rank_variants
#788 - Fix nf-core pipelines download not working in newer versions (3.4.1+)

Parameters

Old parameter	New parameter
`--sv_caller`	`--sv_callers`
	`--sv_callers_to_run`
	`--sv_callers_to_merge`
	`--sv_callers_merge_priority`
	`--methylation_call_regions`
	`--snv_call_regions`
	`--sv_call_regions`
	`--qc_regions`
	`--pre_vep_snv_filter_expression`
	`--extra_yak_options`
`--hificnv_excluded_regions`	`--cnv_excluded_regions`
`--hificnv_expected_xx_cn`	`--cnv_expected_xx_cn`
`--hificnv_expected_xy_cn`	`--cnv_expected_xy_cn`
	`--force_sawfish_joint_call_single_samples`

Note

Module updates

Tool	Old version	New version
bedtools/split		2.31.1
severus	1.3	1.6
strdust	0.11.1	0.11.4
hifiasm	0.24.0	0.25.0
echtvar/anno	0.2.0	0.2.2
genmod	3.9	3.10.1
gunzip	1.1	1.13
tabix	1.2	1.21
multiqc	1.25.1	1.28
bcftools/annotate	1.2	1.22
bcftools/concat	1.2	1.22
bcftools/index	1.2	1.22
bcftools/merge	1.2	1.22
bcftools/norm	1.2	1.22
bcftools/query	1.2	1.22
bcftools/reheader	1.2	1.22
bcftools/sort	1.2	1.22
bcftools/stats	1.2	1.22
bcftools/view	1.2	1.22
samtools/convert	1.2	1.22.1
samtools/faidx	1.2	1.22.1
samtools/fastq	1.2	1.22.1
samtools/import	1.2	1.22.1
samtools/index	1.2	1.22.1
samtools/merge	1.2	1.22.1
samtools/sort	1.2	1.22.1
samtools/view	1.2	1.22.1
ensemblvep/filtervep	113	115.2
minimap2	2.28	2.29
deepvariant	1.8.0	1.9.0
paraphase	3.2.1	3.3.4
longphase/haplotag	1.7.3	2.0
longphase/phase	1.7.3	2.0
minimap2 (paraphase)	2.29	2.30
multiqc	1.28	1.31
samtools (paraphase)	1.21	1.22.1
cramino	0.14.5	1.1.0
modkit/bedmethyltobigwig		0.5.1-rc1
sawfish/discover		2.2
sawfish/jointcall		2.2
trgt/merge	3.0.0	4.0.0
trgt/genotype	3.0.0	4.0.0
whatshap/haplotag	2.3	2.8
whatshap/phase	2.3	2.8
whatshap/stats	2.3	2.8

Note

0.7.2 - [2025-10-31]

`Fixed`

#796 - Fixed sorting of phase blocks GTF file

0.7.1 - [2025-07-01]

`Changed`

#714 - Changed file ending restrictions on echtvar_snv_databases and svdb_sv_databases to allow for TSV, JSON and YAML formats in addition to CSV.

0.7.0 - [2025-06-23]

`Changed`

#711 - Updated Stranger and TRGT versions

`Fixed`

#711 - Fixed annotated repeats counting all motifs (not just pathogenic) towards the count that sets STR_STATUS, resulting in false positives

Module updates

Tool	Old version	New version
trgt	1.2.0	3.0.0
stranger	0.9.4	0.9.5

0.6.5 - [2025-05-16]

`Fixed`

#701 - Fixed family VCF merging for single samples when using STRdust as repeat caller

0.6.4 - [2025-05-16]

`Fixed`

#698 - Fixed unstable CALL_PARALOGS test snapshots
#698 - Fixed unstable samplesheet_multisample_bam test snapshots by sorting hiphase variants

0.6.3 - [2025-05-14]

`Added`

#694 - Added CALL_PARALOGS test to CI, missed in #688

`Fixed`

#694 - Fixed bcftools norm not removing duplicate sites

0.6.2 - [2025-05-12]

`Added`

#688 - Added nf-test for CALL_PARALOGS

`Changed`

#688 - Changed the location of test samplesheets to assets/ from genomic-medicine-sweden/test-datasets to make them more flexible to update,
#688 - Updated test data and tests with an extra paraphase region, OR1D5 on chr17
#688 - Changed samples in assets/samplesheet_multisample_bam.csv from HG002 to HG003 due to updates in test data

`Fixed`

#688 - Fixed paraphase VCF merging only containing variants from one region (#683)
#688 - Fixed paraphase JSON merging only containing information from one sample (#689)

`Removed`

#688 - Removed per-sample merging in CALL_PARALOGS

0.6.1 - [2025-04-11]

`Changed`

#657 - Changed phase block output format from tsv to gtf
#676 - Changed to max_sv_size 999999999 in VEP config

`Fixed`

#657 - Fixed bug in whatshap stats in full-sized data (#655)
#676 - Fixed pipeline failing due to variants ending up with no CSQ, since max_sv_size in VEP was too low (#605)

0.6.0 - [2025-04-09]

`Added`

#601 - Added stub to BUILD_INTERVALS
#601 - Added stub to SPLIT_BED_CHUNKS
#606 - Added bgzip and tabix blocks.tsv from whatshap/stats
#609 - Added runtime estimates to documentation
#611 - Added stub to YAK
#618 - Added peddy (https://github.com/brentp/peddy)
#620 - Added words to vscode spellchecker
#621 - Added STRdust caller for short tandem repeat expansions
#621 - Added --str_caller parameter
#638 - Added feature to output alignments as CRAM using --alignment_output_format parameter
#646 - Added link to genomic-medicine-sweden/nallorefs in documentation

`Changed`

#591 - Updated version to 0.6.0dev
#592 - Updated local and nf-core modules to fix Nextflow language server issues
#593 - Updated local subworkflow to fix Nextflow language server issues
#603 - Updated the samtools/fastq module to add stub
#604 - Changed all .join() to include failOnMismatch:true, failOnDuplicate:true where possible
#611 - Updated splitubam module to fix stubs
#619 - Updated gfastats to fix Nextflow language server issues
#621 - Renamed parameter --trgt_repeats to --str_bed.
#621 - Updated preset ONT_R10 to enable repeat expansion calling by default.
#621 - Changed repeat annotation workflow to run by default if and only if repeat expansions were called with TRGT.
#640 - Updated nf-test paths that were broken by #626
#645 - Updated metro map with peddy and STRdust
#647 - Updated version to 0.6.0

`Removed`

#620 - Removed args from local modules that doesn't use it
#625 - Removed last .first() from versions, that resulted in a warning displayed when running the pipeline
#632 - Removed most of docs/index.md to avoid duplication with README.md

`Fixed`

#595 - Fixed unstable assembly outputs when there's multiple input files per sample
#620 - Fixed spelling mistakes
#626 - Fixed pipeline lint local_component_structure warnings
#637 - Fixed test without target regions not triggering on PRs to the master branch
#639 - Fixed groupTuple bottleneck in ALIGN_ASSEMBLIES
#644 - Fixed FastQC ignoring memory parameter
#653 - Fixed merge mistakes when squashing release 0.5.0
#754 - Fixed missing file in .prettierignore

Parameters

Old parameter	New parameter
	`--str_caller`
`--trgt_repeats`	`--str_bed`
	`--skip_peddy`
	`--peddy_sites`
	`--alignment_output_format`

Note

Module updates

Tool	Old version	New version
gfastats	1.3.6	1.3.10
add_most_severe_consequence	1.0	1.1
add_most_severe_pli	1.0	1.1
peddy		0.4.8
strdust		0.11.1

Note

0.5.2 - [2025-03-27]

`Fixed`

#634 - Fixed SVDB process error when sample and family_id was named the same (#633)

0.5.1 - [2025-03-10]

`Fixed`

#607 - Fixed repeat annotation not working with multiple individuals per family (#562)

Module updates

Tool	Old version	New version
stranger	0.9.2	0.9.4

Note

0.5.0 - [2025-03-03]

`Added`

#549 - Added merging of paraphase JSON and VCF files into family files
#516 - Added beta support for ONT R10 assembly
#531 - Added missing credits to the README
#537 - Added per-base depth output in d4 format from mosdepth
#542 - Added a hidden parameter --publish_unannotated_family_svs
#544 - Added --skip_sv_calling parameter to skip sv_calling subworkflow
#574 - Added contributors to nextflow.config
#578 - Added back help texts, fixing lint warning

`Changed`

#532 - Updated template to nf-core/tools version 3.1.1
#533 - Updated the fastqc module
#535 - Updated DeepVariant to 1.8.0 for SPRQ compatibility
#536 - Downgraded Sniffles from 2.0.7 to 1.0.12 due to missing calls
#541 - Updated template to nf-core/tools version 3.1.2
#542 - Changed to always use all SV callers, but only take variants from one of them forward, set by --sv_caller
#545 - Changed CI to use latest-stable version of Nextflow instead of latest-everything
#556 - Changed family-level SNVs naming to snvs from snv, matching sample-level and other variants
#557 - Updated Severus to version 1.3
#558 - Changed VEP to single-threaded by default, because of Ensembl/ensembl-vep#1759
#560 - Updated template to nf-core/tools version 3.2.0
#566 - Replaced dipcall with ALIGN_ASSEMBLIES, mostly mimicking the alignment part of dipcall, while omitting the variant calling. Updated docs and output files.
#572 - Changed CALL_SVS to sort sniffles1 variants, which could be unsorted by default
#573 - Updated metro-map to reflect changes to sniffles and dipcall
#576 - Merged master back to dev
#577 - Updated docs/index.md to match README.md
#580 - Changed CLEAN_SNIFFLES to fix sniffles1 header and DUP/INV end position
#583 - Merged master back to dev
#585 - Updated version to 0.5.0

`Removed`

#533 - Removed local module echtvar encode, not used anymore
#577 - Removed dipcall references missed in #566.
#578 - Removed igenomes code

`Fixed`

#533 - Fixed some Nextflow language server issues
#546 - Fixed output filenames mismatches in documentation compared to pipeline
#556 - Fixed an issue where the pipeline could not run with --skip_snv_annotation
#566 - Fixed wrong minimap2 mapping preset for genome assemblies
#570 - Fixed bug where filtering of SNVs was trying to run even if --skip_snv_calling was active
#578 - Fixed warning about non-existing params.genome when running the pipeline
#580 - Fixed missing nf-test triggers for changes that may affect the entire pipeline
#584 - Fixed pipeline not validating that the samplesheet only contains one project correctly
#586 - Fixed mistake in the usage docs where --target_regions was written as --target_bed

Parameters

Old parameter	New parameter
	`--hifiasm_preset`
	`--skip_sv_calling`
	`--publish_unannotated_family_svs`

Note

Module updates

Tool	Old version	New version
hifiasm	0.19.8	0.24.0
deepvariant	1.6.1	1.8.0
sniffles	2.0.7	1.0.12
mosdepth	0.3.8	0.3.10
paraphase	3.1.1	3.2.1
bcftools merge		1.20
merge_json		1.0
severus	1.1	1.3
dipcall	0.3
tagbam		0.1.0

Note

0.4.1 - [2025-02-17]

`Fixed`

#553 - Fixed pipeline always requiring --vep_cache to run, and clarified documentation
#553 - Fixed process.shell in nextflow.config causing CI runners to fail

0.4.0 - [2025-01-15]

`Added`

#345 - Added first version of a metro map
#346 - Added nf-test to call_svs
#351 - Added sample name to sniffles2 VCF
#352 - Added (hidden) params.extra_<tool>_options for the test profile to modkit, vep, paraphase and hifiasm
#356 - Added missing SNV and PED file to output documentation
#363 - Added Zenodo link
#366 - Added sorting of samples when creating PED files, so the output is always the same
#367 - Added Severus as the default SV caller, together with a --sv_caller parameter to choose caller
#371 - Added FOUND_IN=caller tags to SV output
#388 - Added longphase as the default phaser
#388 - Added single-sample tbi output to the short variant calling subworkflow
#393 - Added a new --minimap2_read_mapping_preset parameter
#403 - Added FOUND_IN=hificnv tags to CNV calling output
#408 - Added a new subworkflow to annotate SVs
#417 - Added FOUND_IN=deepvariant tags to SNV calling output
#418 - Added a check for unique input filenames for each sample
#419 - Added support for SV filtering using input BED file (#348)
#429 - Added nf-test to CNV calling
#429 - Added SVDB to merge CNV calling results
#430 - Added a GitHub action to build and publish docs to GitHub Pages
#431 - Added files needed to automatically build and publish docs to GitHub Pages
#435 - Added nf-test to rank variants
#445 - Added FOUND_IN tag and nf-test to rank variants
#446 - Added the vcfstatsreport from DeepVariant to snv calling
#450 - Added ranking of SVs (and CNVs)
#451 - Added support for running methylation subworkflow without phasing
#451 - Added nf-test to methylation
#491 - Added a changelog reminder action
#496 - Added a subworkflow to filter variants

`Changed`

#344 - Changed version to 0.4.0dev
#346 - Renamed structural_variant_calling to call_svs
#351 - Changed from using sniffles to bcftools to merge SV calls from multiple samples
#351 - Renamed the structural variant output files and directories
#352 - Changed fastq conversion to run only when the assembly workflow is active
#352 - Changed FastQC to run on BAM files to remove concatenation of fastq files
#352 - Changed FastQC from the main workflow to QC_ALIGNED_READS, updated output directories and documentation
#352 - Combined --skip_raw_read_qc and --skip_aligned_read_qc parameters into --skip_qc
#355 - Updated paraphase to compress and index VCFs within the module
#365 - Changed CI to only use nf-test for pipeline tests
#381 - Updated CI nf-test version to 0.9.0
#382 - Changed vep_plugin_files description in schema and docs
#388 - Changed phasing output structure and naming, and updated docs
#393 - Changed the default minimap2 preset for PacBio data from map-hifi to lr:hqae
#397 - Changed pipelines_testdata_base_path to pin a specific commit
#402 - Updated broken test profile link added in #397
#403 - Changed ADD_FOUND_IN_TAG process to allow input files to be named the same as output, fixed header line description and removed bcftools view versions in header
#403 - Revert #404
#404 - Changed to only run nf-tests where files have changes compared to the base branch
#407 - Changed echtvar example file in docs
#410 - Updated genmod to version 3.8.3
#411 - Updated longphase module to most recent version. (#409).
#416 - Updated WhatsHap to 2.3 and added the --use-supplementary flag to use supplementary reads for phasing by default. Changed modules to use biocontainers instead of custom containers. (#296)
#417 - Updated SNV annotation tests to use correct configuration, and snapshot the md5sum, and summary of the variants
#418 - Changed the default value of --alignment_processes from 1 to 8, meaning the pipeline will perform parallel alignment by default
#418 - Changed the order of input files to samtools merge to be sorted on filename, avoiding unstable nf-test snapshots
#422 - Updated nf-core/tools template to v3.0.1
#423 - Updated metro map
#428 - Changed from using bcftools to SVDB for SV merging
#429 - Updated HiFiCNV to 1.0.0
#429 - Refactored the CNV calling subworkflow
#429 - Changed SV and CNV calling outputs, merging is now done per family
#431 - Changed CITATIONS.md to docs/CITATIONS.md,
#433 - Updated docs and README.
#434 - Updated the SVDB merge module to fix unstable CALL_SVS tests
#435 - Updated and refactored processes and workflows related to variant ranking
#438 - Updated pipeline tests to use functions in nft-utils instead of checking hardcoded paths
#440 - Updated hifiasm to 0.20 with new default parameters for telomeres and scaffolding (#295)
#441 - Changed the minimap2 preset for hifi reads back to map-hifi
#443 - Refactored reference channel assignments
#443 - Updated schemas for vep_plugin_files and snp_db
#451 - Simplified methylation subworkflow
#474 - Updated VEP and CADD channels to fix bugs introduced in #443
#479 - Replaced bgzip tabix with bcftools sort in rank variants to fix #457
#480 - Updated ranking of SVs to work with multiple families per project
#484 - Updated metro map and added SVG version
#485 - Updated repeat expansion annotation to annotate per family instead of per sample
#486 - Updated nf-core modules
#487 - Changed CI tests to only run tests where changes have been made
#488 - Changed naming of input parameters
#489 - Updated nf-core template to 3.0.2
#493 - Refactored nallo.nf to remove many nested ifs and easier to follow logic
#493 - Updated rank_variants dependencies with sv_annotation
#498 - Updated CI to fix CI failures after merge
#502 - Changed to annotating and ranking SNVs per family instead of per project
#502 - Changed output documentation and structure to match sample and family for all variants
#502 - Changed the way of validating the samplesheet to remove outputting false errors with ifEmpty
#505 - Updated TRGT to 1.2.0
#506 - Updated documentation
#507 - Changed the default value of ch_hgnc_ids to allow running without --filter_variants_hgnc_ids introduced in #496
#509 - Updated documentation to fix mistakes
#510 - Changed the MultiQC methods description to update dynamically based on ch_versions
#512 - Changed one single_sample to sample and one multi_sample to family output directories missed in #502
#512 - Changed all *_snv_* to *_snvs_* for published output files to match snvs, cnvs, svs and repeats.
#513 - Updated CITATIONS.md link in README
#523 - Updated to filter more than one family per run, missed in #496

`Removed`

#352 - Removed the fqcrs module
#356 - Removed filter_vep section from output documentation since it is not in the pipeline
#379 - Removed VEP Plugins from testdata (genomic-medicine-sweden/test-datasets#16)
#388 - Removed support for co-phasing SVs with HiPhase, as the officially supported caller (pbsv) is not in the pipeline
#412 - Removed bcftools/index, as indexing is handled by other modules and no references remained. (#377)
#502 - Removed support for automatically creating an echvar database with SNVs and INDELs
#502 - Removed contains_affected logic from the snv-calling workflow, since this was previously changed to be checked before pipeline start

`Fixed`

#370 - Fixed unsorted variants in SNV outputs (#362)
#381 - Fixed --vep_cache not working as expected with tar.gz cache downloaded from VEP, updated testdata in genomic-medicine-sweden/test-datasets#17
#382 - Fixed broken links and formatting in documentation
#393 - Fixed minimap2 preset for ONT data being overwritten to map-ont when it should have been lr:hq, due to different settings in index and alignment processes #392
#402 - Fixed double sample names in HiFiCNV output
#438 - Fixed missing/malformed software versions in ADD_FOUND_IN_TAG, ADD_MOST_SEVERE_CSQ, ADD_MOST_SEVERE_PLI, SAMPLESHEET_PED, SOMALIER_PED and TRGT
#444 - Fixed genmod assigning wrong models on chromosome X when named chrX (#343)
#502 - Fixed genmod only scoring compounds in one family #501

Parameters

Old parameter	New parameter
`--skip_aligned_read_qc`	`--skip_qc`
`--skip_raw_read_qc`	`--skip_qc`
	`--sv_caller`
	`--minimap2_read_mapping_preset`
`--genome`
`--igenomes_ignore`
`--max_cpus`
`--max_memory`
`--max_time`
`--validationShowHiddenParams`
`--validationSkipDuplicateCheck`
`--validationS3PathCheck`
`--monochromeLogs`	`--monochrome_logs`
	`--filter_variants_hgnc_ids`
	`--filter_snvs_expression`
	`--filter_svs_expression`
`--skip_short_variant_calling`	`--skip_snv_calling`
`--skip_assembly_wf`	`--skip_genome_assembly`
`--skip_mapping_wf`	`--skip_alignment`
`--skip_methylation_wf`	`--skip_methylation_pileups`
`--skip_phasing_wf`	`--skip_phasing`
`--variant_caller`	`--snv_caller`
`--parallel_snv`	`--snv_calling_processes`
`--cadd_prescored`	`--cadd_prescored_indels`
`--snp_db`	`--echtvar_snv_databases`
`--variant_catalog`	`--stranger_repeat_catalog`
`--bed`	`--target_regions`
`--hificnv_xy`	`--hificnv_expected_xy_cn`
`--hificnv_xx`	`--hificnv_expected_xx_cn`
`--hificnv_exclude`	`--hificnv_excluded_regions`
`--reduced_penetrance`	`--genmod_reduced_penetrance`
`--score_config_snv`	`--genmod_score_config_snvs`
`--score_config_sv`	`--genmod_score_config_svs`
`--parallel_alignments`	`--alignment_processes`
`--svdb_dbs`	`--svdb_sv_databases`

Note

Module updates

Tool	Old version	New version
fqcrs	0.1.0
severus		1.1
longphase		1.7.3
genmod	3.8.2	3.9
WhatsHap	2.2	2.3
SVDB		2.8.2
hifiasm	0.19.8	0.20.0
HiFiCNV	0.1.7	1.0.0
samtools/faidx	1.2	1.21
samtools/index	1.2	1.21
samtools/merge	1.2	1.21
stranger	0.9.1	0.9.2
multiqc	1.21	1.25.1
ensemblvep/filter_vep		113
TRGT	0.4.0	1.2.0
bcftools/merge	1.2

Note

0.3.2 - [2024-09-20]

`Fixed`

#396 - Fixed the release test profile not working, by pinning the testdata used #395

0.3.1 - [2024-09-11]

`Fixed`

#359 - Fixed single sample SNV VCFs containing variants from all samples, resulting in a large number of empty GT calls

0.3.0 - [2024-08-29]

`Added`

#230 - Added nf-test to the short variant calling workflow
#231 - Added initial tests for ONT data
#234 - Added a --deepvariant_model_type parameter to override the model type set by --preset
#239 - Added initial nf-test to the pipeline
#243 - Added nf-test to the short variant annotation workflow
#245 - Added repeat annotation with Stranger
#252 - Added a new SCATTER_GENOME subworkflow
#255 - Added a new RANK_VARIANTS subworkflow to rank SNVs using genmod
#261 - Added a --skip_rank_variants parameter to skip the rank_variants subworkflow
#264 - Added a project column to the sampleheet
#266 - Added CADD to dynamically calculate indel CADD-scores
#270 - Added SNV phasing stats to MultiQC
#271 - Added a --skip_aligned_read_qc parameter to skip the qc aligned reads subworkflow
#314 - Added a --vep_plugin_files parameter to separate VEP plugins from cache
#320 - Added complete citations to CITATIONS.md and MultiQC report

`Changed`

#232 - Changed to softer --preset requirements, non-supported subworkflows can now be explicitly enabled if necessary
#232 - Changed --skip_repeat_wf to default to true for preset ONT_R10
#233 - Changed the CNV calling workflow to allow calling using ONT data
#235 - Changed the ONT_R10 preset to not allow phasing with HiPhase
#240 - Reorganize processes in the snv annotation and short variant calling workflows
#240 - GLNexus multisample output is now decomposed and normalized
#244 - Updated VEP with more annotations
#245 - Merged (multisample) repeats from TRGT is now output even if there's only one sample
#245 - Split the repeat analysis workflow into one calling and one annotation workflow, --skip_repeat_wf becomes --skip_repeat_calling and --skip_repeat_annotation
#246 - Renamed processes and light refactoring of the short variant calling workflow
#246 - Use groupKey to remove bottleneck in the short variant calling workflow
#247 - Updated nft-bam to 0.3.0 and added BAM reads to snapshot
#247 - Changed minimap2 preset from map-ont to lr:hq for --preset ONT_R10
#250 - Run mosdepth with --fast-mode and add to MultiQC report
#251 - Switched from annotating single sample VCFs to annotating a multisample VCF, splitting the VCF per sample afterwards to keep outputs almost consistent
#256 - Changed Stranger to annotate single-sample VCFs instead of a multi-sample VCF
#258 - Updated test profile parameters to speed up tests
#260 - Updated DeepVariant to 1.6.1 and htslib (tabix) to 1.20
#261 - Changed SNV annotation to run in parallel
#261 - Changed SNV output file names and directory structure
#262 - Updated README
#264 - Changed PED file creation from groovy script to process
#264 - Changed all multisample filenames to {project} from samplesheet
#268 - Only output unphased alignments when phasing is off
#268 - Changed alignment output file names and directory structure
#270 - Changed whatshap stats to always run, regardless of phasing software, and changed the output from *.stats.tsv.gz to *.stats.tsv to allow being picked up by MultiQC
#277 - Allowed CNV calling as soon as SNV calling for a sample is finished
#278 - Changed the SNV ranking to run in parallel per region
#300 - Clarified and formatted nallo.nf
#304 - Changed to treat (u)BAM as the primary input by skipping fastq conversion before aligning
#306 - Updated echtvar version
#307 - Changed somalier relate to also run per sample on sampes with unknown sex, removing the need to wait on all samples to finish aligment before starting variant calling
#307 - Changed the removal of n_files from meta from bam_infer_sex to nallo.nf
#308 - Updated nf-core modules, fixed warnings in local modules, added Dockerfile to fqcrs
#312 - Changed echtvar encode database creation to use dynamic ${project} from samplesheet
#313 - Updated calling of variants in non-autosomal contigs for DeepVariant
#314 - Changed VEP annotation added in #244 to not include SpliceAI
#317 - Changed so that --reduced_penetrance and --score_config_snv is required by rank variants and not SNV annotation
#318 - Updated docs and schema to clarify pipeline usage
#321 - Changed the input to BUILD_INTERVALS to have meta.id when building intervals from reference
#323 - Changed parallel_alignment to parallel_alignments in CI tests as well
#330 - Updated README and version bump
#332 - Changed the PED file input to genmod to include inferred sex from somalier
#333 - Updated TRGT to 0.7.0 and added meta.id as output sample name

`Removed`

#237 - Removed the CONVERT_ONT_READNAMES module that was run before calling repeats with TRGT
#238 - Removed the --extra_gvcfs parameter
#243 - Removed VEP report from output files
#257 - Removed obsolete TODO statements
#258 - Removed VCF report from DeepVariant output
#264 - Removed the option to provide extra SNF files to Sniffles with --extra_snfs
#305 - Removed unused local module bcftools view regions
#319 - Removed samtools reset before samtools fastq when converting BAM to FASTQ

`Fixed`

#231 - Fixed certain tags in input BAM files being transferred over to (re)aligned BAM
#252 - Fixed duplicate SNVs in outputs when providing a BED-regions with overlapping regions
#267 - Fixed warning where MODKIT_PILEUP_HAPLOTYPES would be defined more than once
#300 - Fixed missing paraphase version
#427 - Fixed duplicate RG tags in BAM files after mapping from uBAMs (#426).

Parameters

Old parameter	New parameter
`--skip_repeat_wf`	`--skip_repeat_calling`
`--skip_repeat_wf`	`--skip_repeat_annotation`
	`--deepvariant_model_type`
	`--skip_rank_variants`
	`--skip_aligned_read_qc`
	`--cadd_resources`
	`--cadd_prescored`
`--split_fastq`	`--parallel_alignments`
`--extra_gvcfs`
`--extra_snfs`
`--dipcall_par`	`--par_regions`
	`--vep_plugin_files`

Note

Module updates

Tool	Old version	New version
deepvariant	1.5.0	1.6.1
tabix	1.19.1	1.20
echtvar	0.1.7	0.2.0
somalier	0.2.15	0.2.18
TRGT	0.4.0	0.7.0
cadd		1.6.post1
gawk		5.3.0
add_most_severe_consequence		v1.0
add_most_severe_pli		v1.0
create_pedigree_file		v1.0
genmod		3.8.2
stranger		0.9.1
splitubam		0.1.1
fastp	0.23.4

Note

0.2.0 - [2024-06-26]

`Added`

#148 - Added somalier to automatically infer and update the sex of samples, replacing unknown entries with the inferred data. Requires a VCF with known polymorphic sites supplied with --somalier_sites.
#148 - Added a RG tag to BAM-files during alignment with ID:${meta.id} and SM:${meta.id}
#159 - Added the ability to use multiple input files per sample, by splitting and aligning each input file individually, then merging them post-alignment for streamlined processing
#162 - Added paraphase, a "HiFi-based caller for highly similar paralogous genes"
#179 - Added support for running without --fasta, when running subworkflows that do not require a reference genome
#226 - Added file-level output documentation

`Changed`

#146 - Template merge for nf-core/tools v2.14.1
#145 - Bump to new dev version
#151 - Cleaned up TRGT output directory
#152 - Use prefix in modkit module. Bgzip, index and split outputs into phased/unphased directories
#153 - Changed cramino module to use prefix, renamed and moved all cramino outputs into qc_aligned_reads/cramino/
#159 - Clarify the trio-binning genome assembly workflow
#159 - split_fastq now splits on files instead of lines
#159 - Use groupKey to remove bottleneck, where previously all samples had to wait before progressing after alignment
#162 - Use pipelines_testdata_base_path in config
#163 - Updated multiple module versions
#163 - Changed modkit from local to nf-core module
#173 - Rename methylation outputs to prevent it being overwritten
#176 - Renamed whatshap output files and remove output .err file
#176 - Made skip_call_paralogs usable
#176 - Rename and fix raw read qc parameter
#176 - Mosdepth can be run without bed
#176 - Require somalier sites when running the mapping workflow
#177 - Increased samtools merge resources
#183 - Allows paraphase outputs to be bgzipped when calling multiple genes
#185 - Harmonized, indexed and fixed naming of more variant files to vcf.gz + tbi
#212 - Files that are from the same sample are now merged before FastQC

`Removed`

#162 - Removed --skip... default parameters from schema
#163 - Removed RAM limitations from small test profile
#185 - Removed samtools index from repeat calling workflow, as bai is now used in pipeline
#185 - Removed versions.yml output from minimap2 align
#185 - Removed echtvar anno output
#213 - Removed dipcall parameters from test profile

`Fixed`

#156 - Fixed program versions missing in output and MultiQC report
#178 - Fixed the MultiQC report saying the pipeline was part of nf-core
#180 - Fixed nondescriptive error when no vep_cache was supplied

Parameters

Old parameter	New parameter
	`--somalier_sites`
`--split_fastq`	`--split_fastq`
	`--skip_call_paralogs`
`--skip_qc`	`--skip_raw_read_qc`

split_fastq now splits the input files into n files (range 2-999)

Note

Module updates

Tool	Old version	New version
samtools	multiple	1.20
bcftools	multiple	1.20
gfastats	1.3.5	1.3.6
mosdepth	0.3.3	0.3.8
bgzip	1.11	1.19.1
tabix	1.11	1.19.1
somalier		0.2.15
minimap2	2.26	2.28
hifiasm	0.19.5	0.19.8
modkit	0.2.5	0.3.0
paraphase		3.1.1

Note

0.1.0 - [2024-05-08]

Initial release of genomic-medicine-sweden/nallo, created with the nf-core template.

`Added`

Raw read QC with FastQC and FQCRS
Align reads to reference with minimap2
Aligned read QC with cramino and mosdepth
Call SNVs with DeepVariant and merge with GLNexus
Annotate SNVs with echtvar and VEP
Call SVs with Sniffles, tandem repeats with TRGT and CNVs with HiFiCNV
Phase variants and haplotag reads with whatshap or HiPhase
Create methylation pileups with modkit
Assemble genomes with hifiasm
Align assembly to reference and call variants with dipcall

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