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

What’s Changed

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

Full Changelog: 1.1.0…1.1.1

What’s Changed

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

New Contributors

• @adamrtalbot made their first contribution in #360
• @hrydbeck made their first contribution in #364
• @asp8200 made their first contribution in #368
• @EmmaCAndersson made their first contribution in #357

Full Changelog: 1.0.0…1.1.0