v8.1.1

What's Changed

• fix:Liftover broken or uses wrong container by @dennishendriksen in #670
• fix:install can fail if images/resources are located on another device by @dennishendriksen in #670
• chore:create_gnomad.sh update bcftools 1.19 to 1.20 by @dennishendriksen in #670
• chore:create_mmi.sh update minimap2 2.26 to 2.27_v2 by @dennishendriksen in #670

Full Changelog: v8.1.0...v8.1.1

v8.1.0

What's Changed

• fix:coverage out-of-memory by @dennishendriksen in #659
• feat:bump inheritance_20240115.tsv to inheritance_20241211.tsv by @dennishendriksen in #660
• feat:bump HPO and GADO 20240404 to 20240813 by @dennishendriksen in #662
• Update VKGL, ClinVar, Capice model, Straglr, annotSV, BCFtools, inheritance matcher by @bartcharbon in #657
• Fix non-coding plugin warinig + update ReMM resource by @bartcharbon in #664
• Calculate and annotate VIAB by @bartcharbon in #665
• Bump template to 7.1.0 by @bartcharbon in #666
• chore:add online doc link to CLI usage by @dennishendriksen in #667
• Update stranger, decision-tree by @bartcharbon in #668
• Bump nextflow to 24.10.3 by @bartcharbon in #669

Full Changelog: v8.0.0...v8.1.0

v8.0.0

Breaking changes:

• Default VIP report template requires a configuration file, see here.
• metadata.json structure is changed, categoricals need to have a label and a description, INFO fields no longer have a "field" property. example
• All nodes in the decision tree json files need to have a label.
• VIP now uses nanopore as default sequencing platfrom instead on illumina.

What's Changed

• Do not split multiallelic variants in #640
• Replace coverage calculation with mosdepth and use regions file in #644
• Sample sheet HPO validation in #651
• Support filtering incomplete penetrance in sample tree in #642
• Update ClinVar 2024-06-03 to 2024-11-26 in #639
• Update ClinVar resource creation: reduce number of categories and map the rest to Other to improve variant classification
• Update VKGL 2024-04-01 to 2024-07-01 in #639
• Update VKGL resource creation: remove contigs that are not in the reference genome
• Update CAPICE model from v5.1.2-v2 to v5.1.2-v3 in #639
• Update default sv.cutesv.min_support value from 10 to 2 in #647
• Update container dependencies to use Alpine Linux v3.20.3 instead of v3.18.3
• Update container dependencies to use OpenJDK 21 instead of 17 in #638
• Update vcf-decision-tree v4.1.1 to v5.1.2 in #648 and #654
• Update vcf-report v7.0.0 to v7.2.0 in #643
• Update vcf-report-template v6.2.0 to v7.0.6 in #643 and #655
• Updated vip-report-inheritance-matcher v3.1.1 to v3.3.2
• Introduced vcf.report.config parameter to configure vcf.report.template, see here
• Increase vcf_report process memory usage from 4GB to 6GB
• Fix: INFO/STR_STATUS metadata to PER_ALT in #653
• Fix: Travis GitHub pages deploy in #645 and #646
• Implemented HTSJDK tandem repeat workaround for samtools/htsjdk#1718
• Annotate 'old chrom-post-ref-alt' for normalized variants in INFO/OLD_REC
• Replace Illumina with nanopore as default sequencing platform by @bartcharbon in #656

Full Changelog: v7.9.1...v8.0.0

v7.9.1

What's Changed

• Fix #632 .cram not published in fastq workflow by @dennishendriksen in #633
• Fix #634 Sex not passed to Straglr by @dennishendriksen in #635
• Use CNV:TR instead of <STR[num]> to enable VEP annotations & fix unknown sample sex Straglr error by @dennishendriksen in #636
• update inheritance matcher 3.1.1 to fix MT and YL inheritance matching by @bartcharbon in #637

Full Changelog: v7.9.0...v7.9.1

v7.9.0

What's Changed

• update NXF_JVM_ARGS: change -Xmx250m to -Xmx512m by @dennishendriksen in #619
• update fastq config: set 'filter_reads' cpus to 1 by @dennishendriksen in #618
• Bump vip report to v7.0.0 (add sample tree to report) by @bartcharbon in #622
• fix test.sh runner: fail on 'TIMEOUT' state by @dennishendriksen in #623
• FASTQ workflow parallelization improvements by @dennishendriksen in #620
• Add "pcr_performed" param to disable incompatible tools by @bartcharbon in #621
• Fix GADO not working with certain hpo / proband combinations by @bartcharbon in #626
• Filter called variants by user specified bed file by @bartcharbon in #627
• Add Spectre CNV calling by @bartcharbon in #625
• Remove DP filter from sample decision tree by @bartcharbon in #629
• Bump vip version to 7.9.0 by @bartcharbon in #630

Full Changelog: v7.8.0...v7.9.0

v7.8.0

What's Changed

• Support Nanopore adaptive sampling by @dennishendriksen in #613
• Produce CRAM coverage and read depth intermediate outputs by @dennishendriksen in #605
• Add Green-DB annotations (academic use only, disabled by default) by @bartcharbon in #602
• Update gnomAD v4.0 to v4.1 by @dennishendriksen in #600
• Update VKGL 2024-02 to 2024-04 by @dennishendriksen in #608
• Update ClinVar 2024-03-17 to 2024-06-03 by @dennishendriksen in #608
• Update vip-report 6.0.2 to 6.1.0 by @dennishendriksen in #616
• Update Nextflow 23.10.0 to 24.04.2 by @dennishendriksen in #607
• Add vkgl_vus test by @dennishendriksen in #603
• Fix gnomAD VEP plugin: gnomAD_QC can be incorrect by @dennishendriksen in #601
• Fix GADO not executed when no proband column provided by @bartcharbon in #598
• Fix null exception when no HPO provided by @bartcharbon in #599
• Fix #609 Report job can run out of memory by @dennishendriksen in #610
• Fix #611 DeepVariant hangs in rare cases by @dennishendriksen in #612
• Update default process values for deepvariant_call_duo/trio by @dennishendriksen in #617

Full Changelog: v7.7.1...v7.8.0

v7.7.1

What's Changed

• install.sh: suppress git detached head message by @dennishendriksen in #596
• Fix decision tree issues (regarding FLAG and FILE support) by @bartcharbon in #597
• Fix Straglr Repeat Unit match check by @bartcharbon in #597

Full Changelog: v7.7.0...v7.7.1

v7.7.0

What's Changed

• Bump HPO and GADO 20240208 to 20240404 by @dennishendriksen in #590
• Update cuteSV 2.0.3 to 2.1.1 and add all parameters by @dennishendriksen in #591
• Update Straglr to v2 by @bartcharbon in #593
• Update vcf-report 6.0.1 to 6.0.2 by @dennishendriksen in #594

Full Changelog: v7.6.1...v7.7.0

v7.6.1

What's Changed

• Fix straglr issues, sync philres straglr changes, output straglr tsv as intermediate by @bartcharbon in #589

Full Changelog: v7.6.0...v7.6.1

v7.6.0

What's Changed

• Update VKGL to feb 2024 version by @bartcharbon in #577
• Update minimap 2.26 -> 2.27 + update preset by @bartcharbon in #578
• docs:add link to vip web interface by @dennishendriksen in #580
• Update README.md by @dennishendriksen in #582
• fix:install.sh re-installs inheritance resource by @dennishendriksen in #581
• test:update vkgl test data by @dennishendriksen in #584
• Updated README requirements to be equal to docs by @svandenhoek in #587
• Update GADO and HPO to v2024-02-08 by @dennishendriksen in #585
• Update ClinVar and update CAPICE model to v5.1.2-v2 by @bartcharbon in #586
• VIP 7.6.0 - update inheritance by @bartcharbon in #588

Full Changelog: v7.5.0...v7.6.0