nf-core/raredisease: Changelog The format is based on Keep a Changelog
and this project adheres to Semantic Versioning .
2.6.0 - Cacofonix [2025-06-25]
A feature to start the workflow from duplicate-marked bam files #682
A functionality to take spring files as input #678
Refactored code to only handle clinical variants in the generate_clinical_set workflow #693
Refactored schema_input.json and nextflow_schema.json to improve the error messages and validations of the pipeline #692
Updated add_most_severe_consequence and add_most_severe_pli to fix spelling and language server warnings #689
Refactored code to address issues highlighted by language server #688
Changed for loop to each in create_pedigree_file #683
Refactored repeat annotation and updated Stranger #702
Errors due to channel name and structure inconsistencies in the sentieon SNV calling subworkflow#688
Old parameter
New parameter
skip_haplogrep3
skip_tools
skip_fastp
skip_gens
skip_germlinecnvcaller
skip_peddy
skip_smncopynumbercaller
skip_vcf2cytosure
skip_me_calling
skip_subworkflows
skip_me_annotation
skip_mt_annotation
skip_mt_subsample
skip_repeat_annotation
skip_repeat_calling
skip_snv_annotation
skip_snv_calling
skip_sv_annotation
skip_sv_calling
Tool
Old version
New version
DeepVariant
1.6.1
1.8.0
add_most_severe_consequence
1.0
1.1
add_most_severe_pli
1.0
1.1
stranger
0.9.2
0.9.4
v2.5.0 - Fulliautomatix [2025-05-22]
A new parameter concatenate_snv_calls to generate a concatenated VCF file containing unannotated nuclear & mitochondrial SNV calls #699
Functionality to check contamination in samples using VerifyBamID2 #701
New parameters verifybamid_svd_bed, verifybamid_svd_mu, and verifybamid_svd_ud to supply reference files for VerifyBamID2 #701
Default to remove mitochondrial variants with FILTER status not equal to PASS #697
Sort the input files before vcf2cytosure is invoked #697
Use '--mitochondria-mode' by default when running Gatk4 FilterMutectCalls on mitochondrial variants#697
Old parameter
New parameter
concatenate_snv_calls
verifybamid_svd_bed
verifybamid_svd_mu
verifybamid_svd_ud
Tool
Old version
New version
VerifyBamID2
2.0.1
2.4.0 - Vitalstatistix [2025-02-24]
Add markduplicates metrics to multiqc #679
Update SVDB/merge to fix language server problems #684
Old parameter
New parameter
Tool
Old version
New version
2.3.0 - Getafix [2025-02-13]
A new option skip_haplogrep3 to skip haplogrep3 #675
A new analysis option mito to call and annotate only mitochondrial variants #608
An option extract_alignments to restrict analysis to specific contigs #644
Fastp and ngsbits output files as input of MultiQC #647 .
Haplocheck output file as input of MultiQC #662
Only Structural variants that PASS the filter will be reported and annotated #673
Update haplogrep to v3.2.2 #672
d4 files are not generated by default anymore #648
Suffix used to identify unique fastq pairs from "_T" to "_LNUMBER" #638
Merge output from germlinecnvcaller #635
Update tools #623
Update output file name prefix for upd and chromograph to sample-based #620
Update tools #619
Report only variants above 5% heteroplasmy in the clinical vcf file for mitochondria #616
Download tests #667
Restrict deepvariant analysis of WES samples to bait regions #633 , #658
bcftools annotate declaration in annotate CADD subworkflow #624
Rhocallviz subworkflow will only be invocated once per sample #621
Updated createCaseChannel function to include a check for maternal and paternal ids being set to a numeric 0 #643
Fixed issue of parsing sample sex in the configs #659
Fixed how meta.id was set for input files, giving the resulting files clearer filenames #661
Old parameter
New parameter
extract_alignments
restrict_to_contigs
skip_haplogrep3
Tool
Old version
New version
bcftools
1.18
1.20
ensemblvep
112
110
genmod
3.8.2
3.9
haplogrep
2.4.0
3.2.2
mosdepth
0.3.6
0.3.8
multiqc
1.21
1.26
picard
3.1.1
3.3.0
samtools
1.19.2
1.21
sentieon
202308.02
202308.03
stranger
0.8.1
0.9.2
svdb
2.8.1
2.8.2
tabix
1.19.1
1.20
2.2.0 - Dogmatix [2024-09-13]
A new parameter mt_aligner to control which aligner is used to align reads to mitochondria #600
A new parameter par_bed to pass a PAR bed files to deepvariant #598
A new functionality to pass gzipped resources to vcfanno_extra_resources #589
A new parameter vcfanno_extra_resources to pass an extra resource to vcfanno #588
A new parameter scatter_count to control how many interval files are created from a genome (used to parallelize annotations) #585
Print warning messages if user intends to perform ranking when there are no affected samples #579
Two new parameters skip_repeat_annotation and skip_repeat_calling to skip calling and annotation of repeat expansions #574
A new parameter skip_smncopynumbercaller to skip smncopynumbercaller module #574
A new parameter skip_sv_calling to skip sv calling workflow #572
Two new parameters skip_snv_calling and skip_repeat_analysis to skip snv calling and repeat analysis respectively #571
Two new parameters mbuffer_mem and samtools_sort_threads to control resources given to mbuffer and samtools sort in the bwameme module #570
Update default vep container from v110-v112 #609
Default index for vcfanno extra annotation files from tbi to csi #606
Updated the model for Sentieon DNAScope to v1.1 #601
bwameme can no longer be used to align mitochondrial reads #600
Males' X and Y chromosomes will be treated as haploids during variant calling by deepvariant #598
Acceptable type for lane field in the samplesheet from number to string #597
Allow 0 as a valid value for sex in the samplesheet #595
Updated deepvariant to version 1.6.1 #587
Parallelized vcfanno #585
Skip ROH calling with bcftools if there are no affected samples #579
Refactored tool citation list #577
Removed skip_repeat_analysis added in #571 #574
Remove several skip parameters that had been included in the pipeline to avoid failed CI tests (see parameters table below) #574
readcount_intervals parameter is now mandatory for running germlinecnvcaller. #570 Turn off CNVnator, TIDDIT, SMNCopyNumberCaller, Gens, and Vcf2cytosure for targeted analysis #573
Issues that cropped up when aligner and mt_aligner were different #605
Update docs to show 'vep_plugin_files' as a mandatory parameter for SNV annotation #594
Error in SVDB merge when only a single SV caller is run #586
Errors due to misplaced version statements #578
Stub crashes due to peddy reported in #566 [#576](https://github.com/nf-core/raredisease/pull/576]
Docker manifest error from gnu-wget container #570
Citations for bwameme #563
Old parameter
New parameter
mbuffer_mem
mt_aligner
samtools_sort_threads
skip_repeat_calling
skip_snv_calling
skip_sv_calling
skip_eklipse
skip_fastqc
skip_haplocheck
skip_qualimap
skip_smncopynumbercaller
skip_repeat_annotation
scatter_count
vcfanno_extra_resources
Tool
Old version
New version
Deepvariant
1.5.0
1.6.1
ensemblvep
110
112
2.1.0 - Obelix [2024-05-29]
A new aligner, bwameme #553
A new parameter run_mt_for_wes to turn on mitochondrial analysis for targeted analysis #552
A new parameter bwa_as_fallback to switch aligner to bwa in case bwamem2 fails #551
A new parameter skip_me_calling to skip mobile element calling and the subsequent annotation of them #556
Changed valid values for sex according to the PED file format #550
Refactored config files #538
Refactored mobile element annotation subworkflow files #538
Refactored to remove "a process is defined more than once" warning #557
Updated modules #558
Include multiallelic indel sites in CADD scoring jobs #545
Fixed issues with samtools merge not being run on samples sequenced over multiple lanes #538
Fixed join issues in the mobile element calling subworkflow which occured when mobile_element_references were not provided #556
Old parameter
New parameter
bwameme
bwa_as_fallback
run_mt_for_wes
skip_me_calling
:::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.
:::
Tool
Old version
New version
bwa
0.7.17
0.7.18
CADD
1.6.1
1.6.post1
Sentieon
202308.01
202308.02
bwameme
1.0.6
:::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.
:::
2.0.1 - Asterix (Patch) [2024-03-25]
Germlinecnvcaller subworkflow uses the output channel casecalls from germlinecnvcaller module instead of calls which was invalid. #535
2.0.0 - Asterix [2024-03-18]
Use nf-validation plugin for parameter and samplesheet validation #386
A new parameter skip_vep_filter to skip filtering based on vep results #416
A metromap representating the core parts of the pipeline #428
Metromap and logos for light and dark theme #432
New parameters to skip qualimap and eklipse (--skip_qualimap and --skip_eklipse) #436
Fix "there is no process matching config selector warnings" #435
New parameters to skip fastqc and haplocheck (--skip_fastqc and --skip_haplocheck) #438
CNVnator for copy number variant calling #438
A new parameter svdb_query_bedpedbs to provide bedpe files as databases for SVDB query #449
ngsbits samplegender to check sex #453
New workflow for generating cgh files from SV vcfs for interpretation in the CytosSure interpretation software. Turned off by default #456
Fastp to do adapter trimming. It can be skipped using --skip_fastp #457
New workflow for calling insertion of mobile elements #440
GATK CNVCaller uses segments instead of intervals, filters out "reference" segments between the calls, and fixes a bug with how ch_readcount_intervals was handled #472
bwa aligner #474
Add FOUND_IN tag, which mentions the variant caller that found the mutation, in the INFO column of the vcf files #471
A new parameter vep_plugin_files to supply files required by vep plugins #482
New workflow for annotating mobile elements #483
Added a functionality to subsample mitochondrial alignment, and a new parameter skip_mt_subsample to skip the subworkflow #508 .
Chromograph to plot coverage across chromosomes #507
Added a new parameter vep_filters_scout_fmt to supply a bed-like file exported by scout to be used in filter_vep #511 .
Added two new parameters variant_consequences_snv and variant_consequences_sv to supply variant consequence files for annotating SNVs and SVs. #509
Tiddit updated to v3.6.1 #385
Installed the nf-core version of the sentieon/bwamemindex module #397
Installed the nf-core version of the sentieon/bwamem module #398
Installed the nf-core version of the sentieon/readwriter module #399
Installed the nf-core version of the sentieon/datametrics module #400
Installed the nf-core version of the sentieon/dedup module. The dedup module also contains a call to Sentieon's LocusCollector #401
Removing Sentieon-based BQSR. Recent Illumina sequencers tend to provide well-calibrated BQs, so BQSR may not provide much benefit #402
Installed the nf-core version of the sentieon/dnamodelapply module #403
Installed the nf-core version of the sentieon/wgsmetricsalgo module #404
Installed the nf-core version of the sentieon/dnascope module #406
Breaks down mitochondrial analysis workflow into smaller subworkflows that are more modular #419
Replaced the parameter skip_mt_analysis which was used to turn on/off the mitochondrial workflow #419
Adds a new parameter skip_mt_annotation which can be used to turn on/off annotation and ranking for mitochondrial SNVs #419
Changed the name of the parameter from skip_cnv_calling to skip_germlinecnvcaller #435
Check SVDB query input files for existence and correct format #476
Change hardcoded platform value to params.platform in align_MT.config #475
The split into clincial and research VCFs is now done before ranking the varaints #485
Installed the nf-core version of ensemblvep/vep module #482
The filenames of the ranked output VCF files have been changed. See output.md for more information#485
Patched cnvnator module so that the processes didn't have to rerun after a failed run #503 .
Added a local module to generate bed files with variant caller names #505 .
Invalid GATK4 container which caused incorrect singularity downloads with nf-core download nf-core/modules #3668
Make the default cram prefix same as markduplicates prefix #392
Sort ranked SV vcf before indexing with tabix #393
Make target bed file optional for WGS mode (Issue #375 ) #395
Added constraints to block the pipeline from running CollectWgsMetrics on WES samples #396
Updated modules from nf-core #412
If present, remove duplicate entries in probands and upd_children in the meta. #420
Fixes vep starting as many instances as the square of the number of scatters. #405
Replaced the logic where we added an arbitrary substring to keep file names unique after alignment which we then removed using a split operator, with a simple copy operation. #425
Preventing a crash of rhocall annotate in the case of running four individuals whereof two are affected.
Fixed memory qualifier in gatk4 germlinecnvcaller and postprocessgermlinecnvcalls
Fixed wrong process names when outputting versions in ALIGN_SENTIEON and CALL_SNV.
Fixed gens subworkflow #515
Old parameter
New parameter
--cnvnator_binsize
--gens_pon_female
--gens_pon_male
--min_trimmed_length
--mobile_element_references
--mobile_element_svdb_annotations
--mt_subsample_rd
--mt_subsample_seed
--ngsbits_samplegender_method
--rtg_truthvcfs
--run_rtgvcfeval
--sample_id_map
--score_config_mt
--sdf
--pcr_amplification--sentieon_dnascope_pcr_indel_model
--skip_eklipse
--skip_fastqc
--skip_fastp
--skip_gens
--skip_germlinecnvcaller
--skip_haplocheck
--skip_me_annotation
--skip_mt_annotation
--skip_mt_subsample
--skip_peddy
--skip_qualimap
--skip_vcf2cytosure
--skip_vep_filter
--svdb_query_bedpedbs
--variant_consequences_snv
--variant_consequences_sv
--vcf2cytosure_blacklist
--vep_plugin_files
--vep_filters_scout_fmt
--gens_pon
--gens_switch
--skip_cnv_calling
--skip_mt_analysis
:::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.
:::
v1.1.1 - Abu (Patch) [2023-07-26]
Avoids errors thrown by bcftools concat due to sample names in input vcf files not being in same order #388
v1.1.0 - Abu [2023-07-21]
Add GATK's cnv calling pipeline #362
GATK's ShiftFasta to generate all the files required for mitochondrial analysis #354
Feature to calculate CADD scores for indels #325
HmtNote to annotate mitochondria #355
MT del script to detect mitochondrial deletions #349
eKLIPse to identify large mitochondrial deletions #365
UPD+Chromograph to identify and visualize UPD sites and regions in the chromosomes #364 and #366
Added check for presence of case id for each sample in samplesheet #357
Avoiding publishing uncompressed VCF-file from HMTNOTE_ANNOTATE. (The corresponding compressed VCF-file still gets published.) #368
v1.0.0 - Aladdin [2023-06-01] Initial release of nf-core/raredisease, created with the nf-core template.
FastQC read quality control
Read mapping with BWAmem2/Sentieon
Qualimap & Picard tools quality control metrics
Call repeat expansions with ExpansionHunter and Stranger
SNV calling with DeepVariant/Sentieon
SV calling with Manta and TIDDIT
SNV annotation with bcftools roh, vcfanno, and vep
SV annotation with SVDB query and vep
Separate workflow for analysing and annotating mitochondrial variants
Call copy number variants in the SMN gene using SMNCopyNumberCaller