Raredisease Versions Save

Call and score variants from WGS/WES of rare disease patients.

2.1.0

2 weeks ago

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

2.0.1

2 months ago

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

2.0.0

2 months ago

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

1.1.1

10 months ago

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

1.1.0

10 months ago

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

1.0.0

1 year ago