3.0.0 - Mario

What's Changed

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

New Contributors

• @alexiandra97 made their first contribution in #714
• @mashehu made their first contribution in #737
• @ieduba made their first contribution in #743
• @sofiademmou made their first contribution in #779
• @emmadizdarevic made their first contribution in #800
• @benstory made their first contribution in #815
• @ktruve made their first contribution in #811

Full Changelog: 2.6.0...3.0.0

2.6.0 - Cacofonix

What's Changed

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

New Contributors

• @fellen31 made their first contribution in #684
• @kubranarci made their first contribution in #682
• @ShimiraOleg made their first contribution in #692

Full Changelog: 2.5.0...2.6.0

2.5.0 - Fulliautomatix

What's Changed

• concatenate nuclear and mt SNV calls by @ramprasadn in #699
• Add Verifybamid2 by @ramprasadn in #701
• Patch Vitalstatistix by @ramprasadn in #697

Full Changelog: 2.4.0...2.5.0

2.4.0 - Vitalstatistix

What's Changed

• add markdup to multiqc by @ramprasadn in #679

Full Changelog: 2.3.0...2.4.0

2.3.0 - Getafix

What's Changed

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

New Contributors

• @fevac made their first contribution in #662

Full Changelog: 2.2.0...2.3.0

2.2.0 - Dogmatix

What's Changed

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

New Contributors

• @EmelineFavreau made their first contribution in #562
• @irliampa made their first contribution in #584

Full Changelog: 2.1.0...2.2.0

2.1.0 - Obelix

What's Changed

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

Full Changelog: 2.0.1...2.1.0

2.0.1 - Asterix (patch)

What's Changed

• Address the right emit channel from the germlinecnvcaller module (cohortcalls instead of calls) - by @ramprasadn in #536

Full Changelog: 2.0.0...2.0.1

2.0.0 - Asterix

What's Changed

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

New Contributors

• @alkc made their first contribution in #454
• @Jakob37 made their first contribution in #472

Full Changelog: 1.1.1...2.0.0

1.1.1 - Abu (patch)

What's Changed

• Patch release v1.1.1 by @ramprasadn in #388

Full Changelog: 1.1.0...1.1.1