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

v7.5.0

What's Changed

• Fix incorrect ALT allele order after BCFtools merge by @bartcharbon in #568
• Limit memory used by driver job by @bartcharbon in #569
• Fix install script for cases that nextflow already exists by @bartcharbon in #570
• Remove VEP workaround for custom bigwig annotation by @bartcharbon in #571
• Add FAQ for missing read coverage for SV's by @bartcharbon in #572
• Remove support for decision tree labels by @bartcharbon in #573
• Fix: Only run CAPICE if there are variants to do predictions on by @bartcharbon in #574
• Add ReMM and FATHMM-MKL-NC by @bartcharbon in #575
• Remove broken link in documentation by @bartcharbon in #576

Full Changelog: v7.4.0...v7.5.0

v7.4.0

What's Changed

• feat:add vip.sh -v, --version by @dennishendriksen in #554
• Add md5sum for all tests by @bartcharbon in #555
• Bump VEP(111) and ClinVar by @bartcharbon in #556
• Params to customize classification and reporting metadata by @dennishendriksen in #557
• Update key_features.md by @bartcharbon in #559
• Fix: ncER score can be undefined causing warnings in the VEP plugin by @bartcharbon in #560
• change tree order to filter->vkgl->clinvar->gene->chrom by @dennishendriksen in #558
• Fix plugins for features that do not support transcript by @bartcharbon in #561
• Update capice to 5.1.2 by @bartcharbon in #562
• Update decision tree image by @bartcharbon in #564
• Chore/report601 by @bartcharbon in #565
• Reduce memory needed for picard liftover by @bartcharbon in #563

Full Changelog: v7.3.0...v7.4.0

v7.3.0

What's Changed

• Support YL and MT inheritance by @bartcharbon in #551
• Fix minimap out-of-memory errors by @dennishendriksen in #550
• Fix DeepVariant trio calling out-of-memory errors by @dennishendriksen in #548
• Fix VEP plugin warnings by @dennishendriksen in #549
• Fix dissapearing ALT headers by @bartcharbon in #553

Full Changelog: v7.2.1...v7.3.0