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
Full Changelog: 1.1.1...2.0.0
Contributors
fa2k, jemten, and 8 other contributors