What’s Changed

• Add option to use prescored CADD annotations by @ramprasadn in https://github.com/nf-core/raredisease/pull/866
• Add option to specify call for manta by @ramprasadn in https://github.com/nf-core/raredisease/pull/867
• Replace filter_vep with local Python script by @ramprasadn in https://github.com/nf-core/raredisease/pull/870
• Add bwafastalign/index module by @ramprasadn in https://github.com/nf-core/raredisease/pull/877
• Update saltshaker modules by @ieduba in https://github.com/nf-core/raredisease/pull/879
• Add bwafastalign genome aligner support by @ramprasadn in https://github.com/nf-core/raredisease/pull/880
• Update to latest version of nf-core bwameme/mem which follows same input pattern as bwafastalign/mem by @ramprasadn in https://github.com/nf-core/raredisease/pull/881
• Release 3.1.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/855

Full Changelog: https://github.com/nf-core/raredisease/compare/3.0.0...3.1.0

What’s Changed

• nf-test for subworkflows - I by @ramprasadn in https://github.com/nf-core/raredisease/pull/695
• Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/712
• Resolve inconsistencies in schema JSON definitions by @alexiandra97 in https://github.com/nf-core/raredisease/pull/714
• Use distinct output filenames for bcfools and svdb by @alexiandra97 in https://github.com/nf-core/raredisease/pull/716
• Add interval parameter to RetroSeq by @alexiandra97 in https://github.com/nf-core/raredisease/pull/717
• Switch local most severe consequence & pli scripts for the nf-core ones by @ramprasadn in https://github.com/nf-core/raredisease/pull/732
• fix missing env-file issue in a local module by @ramprasadn in https://github.com/nf-core/raredisease/pull/733
• Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/734
• More tests for subworkflows by @ramprasadn in https://github.com/nf-core/raredisease/pull/713
• Replace local subworkflow generate_clinical_set with nf-core VCF_FILTER_BCFTOOLS_ENSEMBLVEP by @peterpru in https://github.com/nf-core/raredisease/pull/727
• Update to new runner size syntax by @mashehu in https://github.com/nf-core/raredisease/pull/737
• Update ROH usage docs by @fellen31 in https://github.com/nf-core/raredisease/pull/738
• Turn off ME calling for mitochondria by @ramprasadn in https://github.com/nf-core/raredisease/pull/741
• Important! Template update for nf-core/tools v3.5.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/744
• Call SVs in mitochondria using mitochondrial alignments from genome alignment by @ramprasadn in https://github.com/nf-core/raredisease/pull/742
• GATK4 germlinecnvcaller / determinegermlinecontigploidy by @rannick in https://github.com/nf-core/raredisease/pull/746
• upate gens by @rannick in https://github.com/nf-core/raredisease/pull/747
• CADD annotation update to support chr prefix by @rannick in https://github.com/nf-core/raredisease/pull/745
• Add option to subsample mitochondria by number of reads by @ramprasadn in https://github.com/nf-core/raredisease/pull/748
• Refactor 1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/749
• Refactor 2 by @ramprasadn in https://github.com/nf-core/raredisease/pull/750
• add sambamba by @rannick in https://github.com/nf-core/raredisease/pull/752
• Refactor - 3 by @ramprasadn in https://github.com/nf-core/raredisease/pull/751
• Remove the usage of parameters in subworkflows by @ramprasadn in https://github.com/nf-core/raredisease/pull/753
• Move reference preparation to main.nf by @ramprasadn in https://github.com/nf-core/raredisease/pull/754
• Fix issue 739 by @ramprasadn in https://github.com/nf-core/raredisease/pull/755
• Remove ext.when logic from configs - I by @ramprasadn in https://github.com/nf-core/raredisease/pull/756
• Fix issue 719: Allow bait padding zero by @peterpru in https://github.com/nf-core/raredisease/pull/757
• Remove ext.when logic from prepare references workflow - I by @ramprasadn in https://github.com/nf-core/raredisease/pull/759
• Remove ext.when logic from prepare references workflow - 2 by @ramprasadn in https://github.com/nf-core/raredisease/pull/760
• Remove ext.when logic from prepare references workflow - 3 by @ramprasadn in https://github.com/nf-core/raredisease/pull/762
• Remove option to run bwamem as fallback aligner by @ramprasadn in https://github.com/nf-core/raredisease/pull/763
• Updates to multiqc by @ramprasadn in https://github.com/nf-core/raredisease/pull/764
• Refactor main.nf by @ramprasadn in https://github.com/nf-core/raredisease/pull/766
• Refactor main-nf -II by @ramprasadn in https://github.com/nf-core/raredisease/pull/768
• remove redundant .first() operations by @ramprasadn in https://github.com/nf-core/raredisease/pull/769
• Add option to set genotypes of MT SNVs and sambamba duplicate filtering by @ramprasadn in https://github.com/nf-core/raredisease/pull/770
• Update modules (topics) by @ramprasadn in https://github.com/nf-core/raredisease/pull/771
• Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/773
• mitosalt test by @ieduba in https://github.com/nf-core/raredisease/pull/743
• Add topic versions to local modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/774
• Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/776
• Remove haplocheck by @ramprasadn in https://github.com/nf-core/raredisease/pull/778
• Remove hmtnote annotate by @sofiademmou in https://github.com/nf-core/raredisease/pull/779
• Update svdb module by @sofiademmou in https://github.com/nf-core/raredisease/pull/781
• Refactor subworkflows and add tests by @ramprasadn in https://github.com/nf-core/raredisease/pull/780
• Add tests for subworkflows -II by @ramprasadn in https://github.com/nf-core/raredisease/pull/782
• Refactor and add tests for subworkflow -III by @ramprasadn in https://github.com/nf-core/raredisease/pull/783
• Gens replace local module by @peterpru in https://github.com/nf-core/raredisease/pull/785
• Migrate file publishing from publishDir to centralized output {} block - I by @ramprasadn in https://github.com/nf-core/raredisease/pull/784
• Migrate file publishing from publishDir to centralized output {} block - II by @ramprasadn in https://github.com/nf-core/raredisease/pull/787
• Migrate file publishing from publishDir to centralized output {} block - III by @ramprasadn in https://github.com/nf-core/raredisease/pull/788
• Migrate file publishing from publishDir to centralized output {} block - IV by @ramprasadn in https://github.com/nf-core/raredisease/pull/789
• Remove redundant tabix calls, and update nf-test nextflow config by @ramprasadn in https://github.com/nf-core/raredisease/pull/790
• Migrate file publishing from publishDir to centralized output {} block - V by @ramprasadn in https://github.com/nf-core/raredisease/pull/791
• Create contribution guidelines, and update citation and usage. by @ramprasadn in https://github.com/nf-core/raredisease/pull/792
• Remove haplogrep3 and qualimap by @ramprasadn in https://github.com/nf-core/raredisease/pull/801
• Fix tags in subworkflow by @emmadizdarevic in https://github.com/nf-core/raredisease/pull/800
• add saltshaker modules by @ieduba in https://github.com/nf-core/raredisease/pull/775
• Dev fixes by @ramprasadn in https://github.com/nf-core/raredisease/pull/799
• Add stub test for scatter_genome subworkflow by @emmadizdarevic in https://github.com/nf-core/raredisease/pull/802
• Add exclude_alt parameter by @ramprasadn in https://github.com/nf-core/raredisease/pull/803
• Remove env variable NXF_SINGULARITY_NEW_PID_NAMESPACE from config by @ramprasadn in https://github.com/nf-core/raredisease/pull/804
• Run UPD only for WGS by @ramprasadn in https://github.com/nf-core/raredisease/pull/806
• Replace save_mapped_as_cram with save_all_mapped_as_cram and save_noalt_mapped_as_cram by @ramprasadn in https://github.com/nf-core/raredisease/pull/807
• vcf2cytosure add genome build switch by @peterpru in https://github.com/nf-core/raredisease/pull/809
• Saltshaker html by @ieduba in https://github.com/nf-core/raredisease/pull/808
• Sync dev with fixes in release 300 branch by @ramprasadn in https://github.com/nf-core/raredisease/pull/819
• fix references in mitosalt config by @ieduba in https://github.com/nf-core/raredisease/pull/818
• fix: sort BAM/BAI inputs to Manta for deterministic sample order by @benstory in https://github.com/nf-core/raredisease/pull/815
• fix(call_snv): swap ch_genome_fasta and ch_genome_fai argument order in CALL_SNV_SENTIEON by @ktruve in https://github.com/nf-core/raredisease/pull/811
• Merge changes & bugfixes in release300 by @ramprasadn in https://github.com/nf-core/raredisease/pull/821
• Add an option to skip multiallelics split step in SNV calling workflows. by @ramprasadn in https://github.com/nf-core/raredisease/pull/823
• Release 3.0.0. review comments by @ramprasadn in https://github.com/nf-core/raredisease/pull/827
• extend vcfanno sanity check by @ramprasadn in https://github.com/nf-core/raredisease/pull/834
• Fix issues in call_sv_MT & extend vcfanno sanity check by @ramprasadn in https://github.com/nf-core/raredisease/pull/837
• review comments by @ramprasadn in https://github.com/nf-core/raredisease/pull/840
• Release review comments - III by @ramprasadn in https://github.com/nf-core/raredisease/pull/841
• Bug fix: Convert a channel to value from queue by @ramprasadn in https://github.com/nf-core/raredisease/pull/842
• Bug fix: Run mitosalt for all samples by @ramprasadn in https://github.com/nf-core/raredisease/pull/843
• Release v3.0.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/825

New Contributors

• @alexiandra97 made their first contribution in https://github.com/nf-core/raredisease/pull/714
• @mashehu made their first contribution in https://github.com/nf-core/raredisease/pull/737
• @ieduba made their first contribution in https://github.com/nf-core/raredisease/pull/743
• @sofiademmou made their first contribution in https://github.com/nf-core/raredisease/pull/779
• @emmadizdarevic made their first contribution in https://github.com/nf-core/raredisease/pull/800
• @benstory made their first contribution in https://github.com/nf-core/raredisease/pull/815
• @ktruve made their first contribution in https://github.com/nf-core/raredisease/pull/811

Full Changelog: https://github.com/nf-core/raredisease/compare/2.6.0...3.0.0

What’s Changed

• Update SVDB/merge module to fix language server problems by @fellen31 in https://github.com/nf-core/raredisease/pull/684
• Replace for loop in create_pedigree_file by @fellen31 in https://github.com/nf-core/raredisease/pull/683
• Skip alignment - start from bam files by @kubranarci in https://github.com/nf-core/raredisease/pull/682
• Update deepvariant to 1.8.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/687
• Address language server issues by @ramprasadn in https://github.com/nf-core/raredisease/pull/688
• Fix spelling and language server warnings by @fellen31 in https://github.com/nf-core/raredisease/pull/689
• Handle spring file inputs by @ramprasadn in https://github.com/nf-core/raredisease/pull/678
• Replace several skip_ parameters with a single skip_tools parameter by @ramprasadn in https://github.com/nf-core/raredisease/pull/690
• Json schema improvements by @ShimiraOleg in https://github.com/nf-core/raredisease/pull/692
• Refactor generate_clinical_set subworkflow by @ramprasadn in https://github.com/nf-core/raredisease/pull/693
• Replace several skip parameters with a skip_subworkflows parameter by @ramprasadn in https://github.com/nf-core/raredisease/pull/694
• Merge master (2.5.0) to dev by @ramprasadn in https://github.com/nf-core/raredisease/pull/704
• Refactor repeat annotation by @fellen31 in https://github.com/nf-core/raredisease/pull/702
• Template update to 3.3.1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/707
• Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/705
• Fix issues in dev by @ramprasadn in https://github.com/nf-core/raredisease/pull/709
• Release v2.6.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/708

New Contributors

• @fellen31 made their first contribution in https://github.com/nf-core/raredisease/pull/684
• @kubranarci made their first contribution in https://github.com/nf-core/raredisease/pull/682
• @ShimiraOleg made their first contribution in https://github.com/nf-core/raredisease/pull/692

Full Changelog: https://github.com/nf-core/raredisease/compare/2.5.0...2.6.0

What’s Changed

• concatenate nuclear and mt SNV calls by @ramprasadn in https://github.com/nf-core/raredisease/pull/699
• Add Verifybamid2 by @ramprasadn in https://github.com/nf-core/raredisease/pull/701
• Patch Vitalstatistix by @ramprasadn in https://github.com/nf-core/raredisease/pull/697

Full Changelog: https://github.com/nf-core/raredisease/compare/2.4.0...2.5.0

What’s Changed

• add markdup to multiqc by @ramprasadn in https://github.com/nf-core/raredisease/pull/679

Full Changelog: https://github.com/nf-core/raredisease/compare/2.3.0...2.4.0

What’s Changed

• Bumpversion 2.2.0->2.3.0dev by @ramprasadn in https://github.com/nf-core/raredisease/pull/610
• Add option to analyse only mitochondria by @ramprasadn in https://github.com/nf-core/raredisease/pull/608
• 5% frequency threshold for mitochondrial clinical vcfs by @ramprasadn in https://github.com/nf-core/raredisease/pull/616
• allow vep 112 by @jemten in https://github.com/nf-core/raredisease/pull/617
• Minor fixes by @ramprasadn in https://github.com/nf-core/raredisease/pull/618
• update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/619
• Change output file prefix for upd and chromograph by @ramprasadn in https://github.com/nf-core/raredisease/pull/620
• Invoke rhocallviz subworkflow only once per sample. by @ramprasadn in https://github.com/nf-core/raredisease/pull/621
• Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/623
• Fix channel declaration error in the cadd subworkflow by @ramprasadn in https://github.com/nf-core/raredisease/pull/624
• Update genmod and multiqc by @ramprasadn in https://github.com/nf-core/raredisease/pull/625
• template update 3.0.1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/629
• Important! Template update for nf-core/tools v3.0.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/628
• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/630
• ensure string comparison by @jemten in https://github.com/nf-core/raredisease/pull/632
• add bait regions to deepvariant for WES by @ramprasadn in https://github.com/nf-core/raredisease/pull/633
• Merge germlinecnvcaller output by @ramprasadn in https://github.com/nf-core/raredisease/pull/635
• Raredisease: Add fastp output to multiqc by @peterpru in https://github.com/nf-core/raredisease/pull/637
• Fix fastqc samplenames in multiqc report by @ramprasadn in https://github.com/nf-core/raredisease/pull/638
• Vep update to 113 by @ramprasadn in https://github.com/nf-core/raredisease/pull/639
• Use target bed files as regions instead of bait intervals for SNV calling in WES samples by @ramprasadn in https://github.com/nf-core/raredisease/pull/636
• Upd fix by @jemten in https://github.com/nf-core/raredisease/pull/643
• Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/646
• Add option to restrict analysis to specific contigs by @ramprasadn in https://github.com/nf-core/raredisease/pull/644
• add fastp and ngsbits to multiqc input by @peterpru in https://github.com/nf-core/raredisease/pull/647
• Fix tests by @ramprasadn in https://github.com/nf-core/raredisease/pull/648
• patch vep 110 by @ramprasadn in https://github.com/nf-core/raredisease/pull/649
• Sync v3.1.1 of nf-core template by @ramprasadn in https://github.com/nf-core/raredisease/pull/655
• Important! Template update for nf-core/tools v3.1.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/654
• Remove suffixes sample name in repeat call vcfs by @ramprasadn in https://github.com/nf-core/raredisease/pull/657
• Update module MultiQC to version 1.26 by @peterpru in https://github.com/nf-core/raredisease/pull/660
• padding bed file by @jemten in https://github.com/nf-core/raredisease/pull/658
• Fix sex by @jemten in https://github.com/nf-core/raredisease/pull/659
• Pre release PR1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/664
• set meta.id for some input files by @jemten in https://github.com/nf-core/raredisease/pull/661
• Add haplocheck to multiqc by @fevac in https://github.com/nf-core/raredisease/pull/662
• Pre release PR2 by @ramprasadn in https://github.com/nf-core/raredisease/pull/665
• Fix download tests by @ramprasadn in https://github.com/nf-core/raredisease/pull/667
• Important! Template update for nf-core/tools v3.1.2 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/668
• Review suggestions on v2.3.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/669
• Template update v320 by @ramprasadn in https://github.com/nf-core/raredisease/pull/671
• Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/670
• update haplogrep3 by @ramprasadn in https://github.com/nf-core/raredisease/pull/672
• Keep only SVs that PASS the filter by @ramprasadn in https://github.com/nf-core/raredisease/pull/673
• Update versions by @ramprasadn in https://github.com/nf-core/raredisease/pull/674
• Add option to skip haplogrep3 by @ramprasadn in https://github.com/nf-core/raredisease/pull/675
• Release v2.3.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/666

New Contributors

• @fevac made their first contribution in https://github.com/nf-core/raredisease/pull/662

Full Changelog: https://github.com/nf-core/raredisease/compare/2.2.0...2.3.0

What’s Changed

• typo by @EmelineFavreau in https://github.com/nf-core/raredisease/pull/562
• adds missinf citations for bwameme by @jemten in https://github.com/nf-core/raredisease/pull/563
• Few fixes by @ramprasadn in https://github.com/nf-core/raredisease/pull/570
• Add parameters to skip snv calling and repeat analysis by @ramprasadn in https://github.com/nf-core/raredisease/pull/571
• Add a new paramter to skip sv calling by @ramprasadn in https://github.com/nf-core/raredisease/pull/572
• Turn off workflows irrelevant for WES analysis by @ramprasadn in https://github.com/nf-core/raredisease/pull/573
• Refactor by @ramprasadn in https://github.com/nf-core/raredisease/pull/574
• update peddy module by @ramprasadn in https://github.com/nf-core/raredisease/pull/576
• Refactor citations by @ramprasadn in https://github.com/nf-core/raredisease/pull/577
• Fix WES error by @ramprasadn in https://github.com/nf-core/raredisease/pull/578
• Bcftools roh logic update by @ramprasadn in https://github.com/nf-core/raredisease/pull/579
• adds channels to meme mt align by @jemten in https://github.com/nf-core/raredisease/pull/582
• fix: added publishDir mode in raredisease.config by @irliampa in https://github.com/nf-core/raredisease/pull/584
• Reorder SNV annotation subworkflow to improve performance by @ramprasadn in https://github.com/nf-core/raredisease/pull/585
• SV calling error in WES samples by @ramprasadn in https://github.com/nf-core/raredisease/pull/586
• Deepvariant update v1.6.1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/587
• Add an option to pass extra resources to vcfanno by @ramprasadn in https://github.com/nf-core/raredisease/pull/588
• Add feature to pass vcf.gz files as an additional resource for vcfanno by @ramprasadn in https://github.com/nf-core/raredisease/pull/589
• makes 0 an allowed value for sex by @jemten in https://github.com/nf-core/raredisease/pull/595
• Update docs by @ramprasadn in https://github.com/nf-core/raredisease/pull/594
• Change lane type from number to string by @ramprasadn in https://github.com/nf-core/raredisease/pull/597
• Add option to supply bed file with PAR regions & enable haploid analysis for males by @ramprasadn in https://github.com/nf-core/raredisease/pull/598
• bwamem2 for mt by @ramprasadn in https://github.com/nf-core/raredisease/pull/600
• Updating Sentieon DNAscope ml-model by @asp8200 in https://github.com/nf-core/raredisease/pull/601
• Resolve issues that cropped up when aligner and mt_aligner were different by @ramprasadn in https://github.com/nf-core/raredisease/pull/605
• Add option to generate csi index for managed variants by @ramprasadn in https://github.com/nf-core/raredisease/pull/606
• Change platform description and update vcf2cytosure conditional by @ramprasadn in https://github.com/nf-core/raredisease/pull/607
• Updatevep from v110-112 by @ramprasadn in https://github.com/nf-core/raredisease/pull/609
• Release 2.2.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/580

New Contributors

• @EmelineFavreau made their first contribution in https://github.com/nf-core/raredisease/pull/562
• @irliampa made their first contribution in https://github.com/nf-core/raredisease/pull/584

Full Changelog: https://github.com/nf-core/raredisease/compare/2.1.0...2.2.0

What’s Changed

• Bumpversion 2.1.0dev by @ramprasadn in https://github.com/nf-core/raredisease/pull/533
• Update changelog by @ramprasadn in https://github.com/nf-core/raredisease/pull/534
• adding explicit temps by @jemten in https://github.com/nf-core/raredisease/pull/541
• Template update v2.14.1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/548
• Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/547
• Include “other” variants for CADD to analyse multallelic indels by @fa2k in https://github.com/nf-core/raredisease/pull/545
• Refactoring + other issues with cadd and samtools merge by @ramprasadn in https://github.com/nf-core/raredisease/pull/538
• Bwafallback by @ramprasadn in https://github.com/nf-core/raredisease/pull/551
• changed valid values for the sex variable by @sima-r in https://github.com/nf-core/raredisease/pull/550
• Skip mitochondrial analysis for WES by @ramprasadn in https://github.com/nf-core/raredisease/pull/552
• Add bwameme by @ramprasadn in https://github.com/nf-core/raredisease/pull/553
• Fix join issues in ME calling subworkflow by @ramprasadn in https://github.com/nf-core/raredisease/pull/556
• Resolve warnings by @ramprasadn in https://github.com/nf-core/raredisease/pull/557
• updating meta.sex type check by @jemten in https://github.com/nf-core/raredisease/pull/559
• update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/558
• refactor by @ramprasadn in https://github.com/nf-core/raredisease/pull/561
• Release 2.1.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/555

Full Changelog: https://github.com/nf-core/raredisease/compare/2.0.1...2.1.0

What’s Changed

• Address the right emit channel from the germlinecnvcaller module (cohortcalls instead of calls) - by @ramprasadn in https://github.com/nf-core/raredisease/pull/536

Full Changelog: https://github.com/nf-core/raredisease/compare/2.0.0...2.0.1

What’s Changed

• bumpversion to 1.2.0dev by @ramprasadn in https://github.com/nf-core/raredisease/pull/384
• Updating tiddit to v3.6.1 by @asp8200 in https://github.com/nf-core/raredisease/pull/385
• Sync dev to latest master with changes from patch release 1.1.1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/390
• switch to nf-validation for parameter and samplesheet validation by @ramprasadn in https://github.com/nf-core/raredisease/pull/386
• Correct GATK4 container spec by @adamrtalbot in https://github.com/nf-core/raredisease/pull/391
• Make cram prefix same as the default markduplicates prefix by @ramprasadn in https://github.com/nf-core/raredisease/pull/392
• Update documentation by @ramprasadn in https://github.com/nf-core/raredisease/pull/394
• Add constraints to block the pipeline from running CollectWgsMetrics on WES samples by @ramprasadn in https://github.com/nf-core/raredisease/pull/396
• Make target bed file optional for WGS mode by @ramprasadn in https://github.com/nf-core/raredisease/pull/395
• Update sentieon bwamemindex by @asp8200 in https://github.com/nf-core/raredisease/pull/397
• sort ranked SVs before indexing by @ramprasadn in https://github.com/nf-core/raredisease/pull/393
• Installing and calling nf-core/modules version of sentieon/bwamem by @asp8200 in https://github.com/nf-core/raredisease/pull/398
• Replace local version of SENTIEON_READWRITER with nf-core version by @asp8200 in https://github.com/nf-core/raredisease/pull/399
• Replace local version of SENTIEON_DATAMETRICS with nf-core version by @asp8200 in https://github.com/nf-core/raredisease/pull/400
• Replace local version of sentieon-locuscollector and sentieon-dedup by @asp8200 in https://github.com/nf-core/raredisease/pull/401
• Remove sentieon BQSR by @asp8200 in https://github.com/nf-core/raredisease/pull/402
• Replace local version of SENTIEON_DNAMODELAPPLY with nf-core version by @asp8200 in https://github.com/nf-core/raredisease/pull/403
• Replace local version of SENTIEON_WGSMETRICS with nf-core version by @asp8200 in https://github.com/nf-core/raredisease/pull/404
• Add documentation for running without Internet access by @fa2k in https://github.com/nf-core/raredisease/pull/389
• Add sentieon/dnascope from nf-core/modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/406
• Set “0” a default for missing maternal and paternal id in ped file by @ramprasadn in https://github.com/nf-core/raredisease/pull/411
• Update modules to their latest nf-core version by @ramprasadn in https://github.com/nf-core/raredisease/pull/412
• Add skip_vep_filter parameter by @ramprasadn in https://github.com/nf-core/raredisease/pull/416
• Remove duplicate entries from probands and upd_children in meta by @ramprasadn in https://github.com/nf-core/raredisease/pull/420
• Fixes vep starting as many instances as the square of the number of scatters by @ramprasadn in https://github.com/nf-core/raredisease/pull/421
• Update dnascope-module by @asp8200 in https://github.com/nf-core/raredisease/pull/422
• Add a new sample field to meta by @ramprasadn in https://github.com/nf-core/raredisease/pull/425
• Refactor mitochondrial analysis workflow by @ramprasadn in https://github.com/nf-core/raredisease/pull/419
• Template updates v2.10 by @ramprasadn in https://github.com/nf-core/raredisease/pull/431
• add metromap with core elements by @ramprasadn in https://github.com/nf-core/raredisease/pull/428
• Add logo+metromap for both light and dark themes by @ramprasadn in https://github.com/nf-core/raredisease/pull/432
• add skip_qualimap and skip_eklipse parameters by @ramprasadn in https://github.com/nf-core/raredisease/pull/436
• fix warnings and clean up terminal logs by @ramprasadn in https://github.com/nf-core/raredisease/pull/435
• skip haplocheck and fastqc [skip ci] by @ramprasadn in https://github.com/nf-core/raredisease/pull/438
• Add cnvnator subworkflow by @ramprasadn in https://github.com/nf-core/raredisease/pull/434
• addressing #429 by @jemten in https://github.com/nf-core/raredisease/pull/445
• Document which variantcatalogs to use by @jemten in https://github.com/nf-core/raredisease/pull/443
• Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/449
• Fix mem qualifier by @jemten in https://github.com/nf-core/raredisease/pull/451
• Add sex check by @Lucpen in https://github.com/nf-core/raredisease/pull/453
• Fix two instances of wrong process name passed to ch_versions.mix() when running in sentieon mode by @alkc in https://github.com/nf-core/raredisease/pull/454
• feat add fastp by @Lucpen in https://github.com/nf-core/raredisease/pull/457
• Vcf2cytosure by @jemten in https://github.com/nf-core/raredisease/pull/456
• Nf core template update by @jemten in https://github.com/nf-core/raredisease/pull/461
• Important! Template update for nf-core/tools v2.11.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/463
• feat added specific values for some samplesheet params by @Lucpen in https://github.com/nf-core/raredisease/pull/459
• GATK CNVCaller fixes by @Jakob37 in https://github.com/nf-core/raredisease/pull/472
• Updating vcf2cytosure and tiddit cov by @jemten in https://github.com/nf-core/raredisease/pull/470
• Add found_in tag to vcf by @ramprasadn in https://github.com/nf-core/raredisease/pull/471
• Change hardcoded platform value to params.platform in modules/align_MT.config by @alkc in https://github.com/nf-core/raredisease/pull/475
• adds schema for svdb query inputs by @jemten in https://github.com/nf-core/raredisease/pull/476
• Add bwa mem by @ramprasadn in https://github.com/nf-core/raredisease/pull/474
• Fix for getting chr sizes when fai is given by @jemten in https://github.com/nf-core/raredisease/pull/479
• Add mobile element calling to raredisease by @peterpru in https://github.com/nf-core/raredisease/pull/440
• fix number of me channels by @jemten in https://github.com/nf-core/raredisease/pull/481
• Subworkflow for mobile element annotation by @jemten in https://github.com/nf-core/raredisease/pull/483
• Vep update by @ramprasadn in https://github.com/nf-core/raredisease/pull/482
• Add rtgtools by @ramprasadn in https://github.com/nf-core/raredisease/pull/484
• Update RG generation string by @ramprasadn in https://github.com/nf-core/raredisease/pull/487
• refactoring clinical research split by @jemten in https://github.com/nf-core/raredisease/pull/485
• Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/488
• Template update to 2.12 by @ramprasadn in https://github.com/nf-core/raredisease/pull/501
• Important! Template update for nf-core/tools v2.12 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/499
• Vep pli update by @Lucpen in https://github.com/nf-core/raredisease/pull/491
• Refactor code and configs by @ramprasadn in https://github.com/nf-core/raredisease/pull/490
• fix input channel for vcf2cytosure subworkflow by @jemten in https://github.com/nf-core/raredisease/pull/500
• cnvnator patch by @ramprasadn in https://github.com/nf-core/raredisease/pull/503
• update expansionhunter by @ramprasadn in https://github.com/nf-core/raredisease/pull/502
• minor edit to output documentation by @ramprasadn in https://github.com/nf-core/raredisease/pull/504
• Added a local module to generate bed files with variant caller annotations by @ramprasadn in https://github.com/nf-core/raredisease/pull/505
• Update modules by @ramprasadn in https://github.com/nf-core/raredisease/pull/506
• Chromograph viz by @ramprasadn in https://github.com/nf-core/raredisease/pull/507
• Add subsample mt by @ramprasadn in https://github.com/nf-core/raredisease/pull/508
• Add parameter to supply variant consequence files by @ramprasadn in https://github.com/nf-core/raredisease/pull/510
• add new parameter to supply a bed like file for filtering vep results by @ramprasadn in https://github.com/nf-core/raredisease/pull/511
• Add rhocall viz by @ramprasadn in https://github.com/nf-core/raredisease/pull/512
• updating gens subworkflow by @jemten in https://github.com/nf-core/raredisease/pull/515
• Rename outputs by @ramprasadn in https://github.com/nf-core/raredisease/pull/516
• Template update v 2.13 by @ramprasadn in https://github.com/nf-core/raredisease/pull/518
• Important! Template update for nf-core/tools v2.13 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/517
• Normalize repeat expansions by @ramprasadn in https://github.com/nf-core/raredisease/pull/524
• chromograph autozyg by @ramprasadn in https://github.com/nf-core/raredisease/pull/523
• Fix samplenames in smncopynumbercaller by @ramprasadn in https://github.com/nf-core/raredisease/pull/522
• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/raredisease/pull/525
• Add option to annotate vcf2cytosure file with different(customer) ids by @ramprasadn in https://github.com/nf-core/raredisease/pull/521
• modules update by @ramprasadn in https://github.com/nf-core/raredisease/pull/526
• Release prep v2.0.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/527
• Test download cleanup by @ramprasadn in https://github.com/nf-core/raredisease/pull/529
• fix: parameters not resolving properly when igenomes are used by @ramprasadn in https://github.com/nf-core/raredisease/pull/530
• Release 2.0.0 by @ramprasadn in https://github.com/nf-core/raredisease/pull/528

New Contributors

• @alkc made their first contribution in https://github.com/nf-core/raredisease/pull/454
• @Jakob37 made their first contribution in https://github.com/nf-core/raredisease/pull/472

Full Changelog: https://github.com/nf-core/raredisease/compare/1.1.1...2.0.0

What’s Changed

• Patch release v1.1.1 by @ramprasadn in https://github.com/nf-core/raredisease/pull/388

Full Changelog: https://github.com/nf-core/raredisease/compare/1.1.0...1.1.1

What’s Changed

• Annotate small indels with CADD scores by @ramprasadn in https://github.com/nf-core/raredisease/pull/325
• convert bam to cram by @ramprasadn in https://github.com/nf-core/raredisease/pull/340
• Add shiftfasta by @ramprasadn in https://github.com/nf-core/raredisease/pull/354
• feat added MT deletion script by @Lucpen in https://github.com/nf-core/raredisease/pull/349
• Adding upd by @hrydbeck in https://github.com/nf-core/raredisease/pull/364
• Add ek by @Lucpen in https://github.com/nf-core/raredisease/pull/365
• add chromograph by @ramprasadn in https://github.com/nf-core/raredisease/pull/366
• Update to template 2.9 by @ramprasadn in https://github.com/nf-core/raredisease/pull/372
• Avoid publishing uncompressed VCF-file from HMTNOTE_ANNOTATE by @asp8200 in https://github.com/nf-core/raredisease/pull/368
• added check for case id by @EmmaCAndersson in https://github.com/nf-core/raredisease/pull/357
• Gatkcnvcaller by @ramprasadn in https://github.com/nf-core/raredisease/pull/362
• Update schema, output.md, and remove unused parameters by @ramprasadn in https://github.com/nf-core/raredisease/pull/373
• update eklipse by @ramprasadn in https://github.com/nf-core/raredisease/pull/374

New Contributors

• @adamrtalbot made their first contribution in https://github.com/nf-core/raredisease/pull/360
• @hrydbeck made their first contribution in https://github.com/nf-core/raredisease/pull/364
• @asp8200 made their first contribution in https://github.com/nf-core/raredisease/pull/368
• @EmmaCAndersson made their first contribution in https://github.com/nf-core/raredisease/pull/357

Full Changelog: https://github.com/nf-core/raredisease/compare/1.0.0...1.1.0