genomic-medicine-sweden/nallo: Changelog

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

0.4.0 - [2024-11-22]

`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
#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
#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 outputing 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

`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 containts_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

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
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

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.

0.3.2 - [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, resuling 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 transfered 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

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
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

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.

0.2.0 - [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 subworklows 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

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
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

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.

0.1.0 - [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 assemly to reference and call variants with dipcall

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CHANGELOG.md

CHANGELOG.md

genomic-medicine-sweden/nallo: Changelog

0.4.0 - [2024-11-22]

`Added`

`Changed`

`Removed`

`Fixed`

Parameters

Module updates

0.3.2 - [2024-09-20]

`Fixed`

0.3.1 - [2024-09-11]

`Fixed`

0.3.0 - [2024-08-29]

`Added`

`Changed`

`Removed`

`Fixed`

Parameters

Module updates

0.2.0 - [2024-06-26]

`Added`

`Changed`

`Removed`

`Fixed`

Parameters

Module updates

0.1.0 - [2024-05-08]

`Added`

Files

CHANGELOG.md

Latest commit

History

CHANGELOG.md

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genomic-medicine-sweden/nallo: Changelog

0.4.0 - [2024-11-22]

Added

Changed

Removed

Fixed

Parameters

Module updates

0.3.2 - [2024-09-20]

Fixed

0.3.1 - [2024-09-11]

Fixed

0.3.0 - [2024-08-29]

Added

Changed

Removed

Fixed

Parameters

Module updates

0.2.0 - [2024-06-26]

Added

Changed

Removed

Fixed

Parameters

Module updates

0.1.0 - [2024-05-08]

Added

`Added`

`Changed`

`Removed`

`Fixed`

`Fixed`

`Fixed`

`Added`

`Changed`

`Removed`

`Fixed`

`Added`

`Changed`

`Removed`

`Fixed`

`Added`