What's Changed

Main new features

🧬 Lots of improvements around UMI support (#1937, @SPPearce)
⏩ Parabricks support (#1804, @famosab)
🔍 Muse (#1744, @famosab) and Sentieon TNScope (#1934, @SPPearce)
📜 MSISensor2 (#1965, @maxulysse)
🦖 Varlociraptor (#1940, @famosab)
◀️ Normalization of variants (#1770, @Patricie34 & @maxulysse)
🖖 bbsplit (#1983, @apsteinberg, @tobsecret & @FriederikeHanssen)

Changed

• Version updates:
  • VEP cache updated to v115.2
  • SnpEff updated to v5.3.0a (SnpEff cache downgraded to 99 since 105 is not available at the moment)
  • GATK4 to 4.6.1.0
  • DeepVariant to 1.9.0
  • Freebayes to 1.3.10 with QUAL filtering
• Workflow improvements:
  • Enhanced metro map
  • Doubled default process time
  • Improved sample validation
• Complete test migration:
  • All pytest tests migrated to nf-test framework for better testing infrastructure

Fixed

• Input validation: Better samplesheet validation in #1842 by @nvnieuwk and #1858 by @kjellinjonas and bugfix addReadgroupToMeta in #1849 by @thiago-miller
• CNVkit compatibility: Fixed --no_intervals usage and CPU allocation in #1928 by @SPPearce
• DeepVariant configuration: Added --sample_name argument when meta.sample available in #1992 by @matthdsm

New Parameters

• --freebayes_filter
• --msisensor2_models
• --sentieon_consensus
• --umi_base_skip
• --umi_in_read_header
• --umi_length
• --umi_location
• --umi_tag
• --varlociraptor_chunk_size
• --varlociraptor_scenario_germline
• --varlociraptor_scenario_somatic
• --varlociraptor_scenario_tumor_only

Full Changelog: 3.5.1...3.6.0

What's Changed

Changed

• Bump schema version to 2.2.1 in #1767 by @FriederikeHanssen
• Merge intervals for WES in GATK GenomicsDBImport in #1777 by @tdanhorn

Fixed

• Use file-path-pattern over file-path to hanlde glob for known_indels and known_indels_tbi to fix #1785 in #1797 by @maxulysse
• Update GHA for full_test tests in #1802 by @maxulysse

Full Changelog: 3.5.0...3.5.1

What's Changed

Added

• Tool: Lofreq callparallel by @AitorPeseta and @nevinwu in #1620, #1653, #1752
• Tool: Indexcov by @lindenb in #1613, #1752
• Expose fastp parameter --length_required by @LouisLeNezet in #1660
• Variant Calling tutorial pages to Usage section by @lescai in #1706
• Pipeline level tests by @maxulysse in #1661
• Check if flowcell id matches for paired samples by @pmoris in #1664
• Documentation on how to use WES ASCAT with chr prefixed bed file by @alexanderchang1 in #1638

Changed

• Template update for nf-core/tools v3.0.0, v3.0.1, v3.0.2 by @nf-core-bot in #1680, #1681, #1686
• Update CI actions by @maxulysse in #1657
• Migrate to nf-test by @maxulysse in #1678, #1708, #1731, #1711
• Add nf-test sharding CI by @edmundmiller in #1668
• style: Enable harshilAlignment in VS Code workspace by @edmundmiller in #1730
• Print warnings if flowcell ID cannot be retrieved instead of erroring for Nextflow <24.08.0-edge by @maxulysse in #1673
• Clean up schema file and unhid almost all parameters by @FriederikeHanssen in #1707
• Don't convert input bam files that are supplied in post-alignment steps by @FriederikeHanssen in #1728
• Update all modules by @maxulysse in #1695, #1692, #1663

Fixed

• Fix: template_version_comment GHA by @mirpedrol in #1684
• Fix: flowcell access by @FriederikeHanssen in #1693
• Fix: manifest DOI display on CLI by @maxulysse in #1694
• Fix: nf-schema tests that were not failing on lenient mode by @maxulysse in #1702
• Fix: Missing import statements on error messages(#1566) by @pharmlovex in #1712
• Fix: Convert bcf_annotations.tbi from empty() to value channel to prevent stalling by @bounlu in #1624
• Fix: Add missing spring and ubam files to overview pictures by @FriederikeHanssen in #1734
• Fix: add setup java 17 by @maxulysse in #1743
• Fix: bug where workflow can hang if the email parameter is set. by @robsyme in #1745
• Fix: Sentieon and add docs by @FriederikeHanssen and @edmundmiller in #1746, #1579
• Fix: Update variant calling tool - data type table in docs by @famosab in #1635
• Fix: test string by @FriederikeHanssen in #1754

Removed

• Retire snpeff_genome by @asp8200 in #1656
• Remove Strelka tumor-only somatic variant calling by @nevinwu in #1709
• Remove defaults channel from nf-core conda environments by @maxulysse in #1663
• Remove defaults channel from local modules by @FriederikeHanssen in #1755

New Contributors

• @AitorPeseta made their first contribution in #1620
• @LouisLeNezet made their first contribution in #1660
• @nevinwu made their first contribution in #1653
• @pharmlovex made their first contribution in #1712
• @pmoris made their first contribution in #1664
• @bounlu made their first contribution in #1624
• @alexanderchang1 made their first contribution in #1638
• @lindenb made their first contribution in #1613

Full Changelog: 3.4.4...3.5.0

What's Changed

• FIX: misleading docs - xref 1621 by @maxulysse in #1623
• Correct tower snpeff by @cmatKhan in #1627
• Allow dbsnp if null in germline variant calling by @cmatKhan in #1628

New Contributors

• @cmatKhan made their first contribution in #1627

Full Changelog: 3.4.3...3.4.4

What's Changed

Added

• Add support for fastq.gz.spring-files as input by @asp8200 in #1534, #1573
• Add a specific cnvkit/call module to perform calling from cns files by @lescai in #1502
• Adds the cnvkit/export module, to export called CNVs into VCF by @lescai in #1502

Changed

• Template update for nf-core/tools v2.14.1
• Unify handling of params.cnvkit_reference uniform across the three subworkflows (germline, tumour only, tumour-normal) by @lescai in #1502
• Simplify logic in args management by @maxulysse in #1521
• Update vep cache version to 111 by @maxulysse in #1557
• Cleanup + update modules by @maxulysse in #1545
• Updating documentation by @asp8200 in #1556 and by @maxulysse in #1570

Fixed

• FIX: mapped bam and bai published in the same folder by @asp8200 in #1541
• FIX: typo (strelka2 -> strelka) by @maxulysse in #1536
• FIX: Typo build_from_index -> build_only_index by @maxulysse in #1547
• FIX: Correct vep_cache_path_full when refseq/merged option is present by @YeHW in #1563
• Remove snapshot from Haplotypecaller tests by @maxulysse in #1596
• Remove snapshot from Deepvariant tests by @maxulysse in #1597
• Remove empty outdirs by @FriederikeHanssen in #1612
• Remove legacy configs of CUSTOM_DUMPSOFTWAREVERSIONS by @asp8200 in #1542

New Contributors

• @famosab made their first contribution in #1527
• @YeHW made their first contribution in #1563

Full Changelog: 3.4.2...3.4.3

What's Changed

• 3.5.0dev - back to dev by @maxulysse in #1477
• feat(nf-prov): pin nf-prov to 1.2.2 by @maxulysse in #1482
• Improve cloud testing matrix strategy by @adamrtalbot in #1378
• Add new citation by @FriederikeHanssen in #1485
• Fixing call to GATK4_HAPLOTYPECALLER by @asp8200 in #1488
• Update sentieon modules to 202308.02 by @asp8200 in #1487
• add test data in igenomes by @maxulysse in #1489
• Update mosdepth by @asp8200 in #1490
• feat(wave): add wave profile by @maxulysse in #1493
• handle multiple DOIs by @maxulysse in #1496
• Fix: Cloud Storage objects are immutable on GCP by @maxulysse in #1494
• feat(release): prepare release 3.4.2 by @maxulysse in #1498
• fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests by @maxulysse in #1499
• fix: remove string none option from params.ascat_genome by @kenibrewer in #1501
• Adding Simon and Ken by @maxulysse in #1509
• Update CITATIONS.md with fgbio by @nh13 in #1505
• fix(TYPO): index_alignement should be index_alignment by @nh13 in #1506
• Release 3.4.2 by @maxulysse in #1484

New Contributors

• @kenibrewer made their first contribution in #1501
• @nh13 made their first contribution in #1505

Full Changelog: 3.4.1...3.4.2

https://github.com/nf-core/sarek/blob/master/CHANGELOG.md#342---s%C3%A1jt%C3%A1ristj%C3%A5hkk%C3%A5

What's Changed

• Ncbench by @FriederikeHanssen in #1266
• Back to Dev by @FriederikeHanssen in #1333
• remove extra v for slack report by @FriederikeHanssen in #1334
• add docs for bcftools annotate params by @FriederikeHanssen in #1335
• Update sentieon-modules by @asp8200 in #1339
• enable qc when starting from VC by @FriederikeHanssen in #1344
• Preserve STDERR by @sminot in #1345
• fix params in test profiles by @maxulysse in #1351
• Add Azure megatests by @adamrtalbot in #1340
• Important! Template update for nf-core/tools v2.11 by @nf-core-bot in #1360
• 1357 grouping strategy applied by counting number of FASTQ files generated by FASTP by @adamrtalbot in #1364
• Template update for nf-core/tools version 2.11.1 by @mirpedrol in #1365
• remove params from subworkflows by @maxulysse in #1359
• Add test profile for ncbench by @FriederikeHanssen in #1372
• fix intervals file by @FriederikeHanssen in #1373
• Ncbench by @FriederikeHanssen in #1272
• Ngscheckmate fix by @SPPearce in #1381
• Important! Template update for nf-core/tools v2.12 by @nf-core-bot in #1385
• Update README.md by @maxulysse in #1390
• Fix --three_prime_clip_r{1,2} parameter documentation (fixes #1382) by @tdanhorn in #1383
• Updating sentieon modules by @asp8200 in #1401
• fix dead link by @allaway in #1395
• Fix intervals with dot by @maxulysse in #1403
• add modules_testdata_base_path by @maxulysse in #1409
• update triggered tests by @maxulysse in #1411
• Updating samtools by @asp8200 in #1408
• Update mulled-containers to samtools v1.19.2 by @asp8200 in #1412
• Where is Edmund? by @maxulysse in #1413
• Important! Template update for nf-core/tools v2.13 by @nf-core-bot in #1414
• Fix test name by @maxulysse in #1407
• updating GATK by @asp8200 in #1419
• Removing docker.userEmulation by @asp8200 in #1405
• Make -a a default argument for bcftools concat by @MatthiasZepper in #1420
• ASSESS_SIGNIFICANCE fails with Rscript error fix by @nschcolnicov in #1400
• Template update for nf-core/tools version 2.13.1 by @maxulysse in #1428
• Fix datapath in nftests by @asp8200 in #1426
• Using process.containerOptions instead of docker.runOptions by @asp8200 in #1431
• Dummy PR : testing docker container options in GATK Spark modules by @asp8200 in #1430
• Replacing local module BUILD_INTERVALS with nf-core mdule GAWK by @asp8200 in #1439
• Light refactoring by @maxulysse in #1422
• fix(spark): add a spark profile to set up the docker runOptions by @maxulysse in #1456
• Removing stub option from nf-cmd in the test of pipeline-download by @asp8200 in #1436
• feat(modules): update all modules by @maxulysse in #1457
• prepare 3.4.1 by @maxulysse in #1461
• Ascat fix by @maxulysse in #1462
• fix(CI): add spark profile to all spark tests by @maxulysse in #1463
• Fix call to SENTIEON_DEDUP by @asp8200 in #1465
• feat(modules): update vep to 111.0 by @maxulysse in #1466
• Fixing sentieon - code and tests by @asp8200 in #1469
• Multiqc channels by @maxulysse in #1470
• fix(schema): add some params to validationSchemaIgnoreParams for better handling by @maxulysse in #1471
• fix(vep_cache_version-snpeff_db): both params are string by @maxulysse in #1472
• fix(spark): load spark profile after loading the test profiles by @maxulysse in #1473
• Release 3.4.1 by @maxulysse in #1460

New Contributors

• @sminot made their first contribution in #1345
• @mirpedrol made their first contribution in #1365
• @tdanhorn made their first contribution in #1383
• @allaway made their first contribution in #1395
• @MatthiasZepper made their first contribution in #1420
• @nschcolnicov made their first contribution in #1400

Full Changelog: 3.4.0...3.4.1

What's Changed

New tools:

• Dnascope was added by @asp8200 in #1193, #1280
• Add NGSCheckMate by @SPPearce in #1252
• Add CnvkKt Genemetrics by @grantn5 in #1223
• Add Bcftools annotate by @grantn5 in #1267

Refactoring

• Add an nf-test CI by @adamrtalbot in #1288, #1289, #1290
• Created subworkflow for parsing samplesheet with nf-test by @RaqManzano in #1286
• Update config files and other minor code polishing by @maxulysse in #1325

Bug fixes and other updates

• Fix bug with params.json file writing on s3 by @FriederikeHanssen in #1318
• Fix links to docs by @maxulysse in #1328
• Fix nf-prov usage by @maxulysse in #1301
• Fix remove use_annotation_cache_keys params by @maxulysse in #1298
• Fix clashes of config of FILTERVARIANTTRANCHES in different subworkflows by @asp8200 in #1315
• Fix several bugs for joint calling with Mutect2 by @FriederikeHanssen & @maxulysse in #1277, #1309
• Update modules by @maxulysse & @FriederikeHanssen in #1304, #1311, #1327
• Add SnpEff to full sized tests by @FriederikeHanssen in #1330
• Proper usage of vep_version by @maxulysse in #1303
• Update docs by @FriederikeHanssen in #1278, #1317
• Adding labels to the local modules by @asp8200 in #1287

New Contributors

• @grantn5 made their first contribution in #1223
• @RaqManzano made their first contribution in #1286
• @SPPearce made their first contribution in #1252

Full Changelog: 3.3.2...3.4.0

What's Changed

• back to dev by @FriederikeHanssen in #1246
• fix result path by @FriederikeHanssen in #1247
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #1254
• FIX: remove spaces in controlfreec modules by @maxulysse in #1256
• FEAT: Improve documentation for annotation cache by @maxulysse in #1248
• Add nf-prov by @maxulysse in #1259
• FEAT: add merge to cache checks by @maxulysse in #1261
• FEAT: prepare RC 3.3.2 by @maxulysse in #1262
• FIX: revert controlfreec-assesssignificance by @maxulysse in #1270
• FEAT: Release Canditate 3.3.2 by @maxulysse in #1264

Full Changelog: 3.3.1...3.3.2

What's Changed

• FIX: Zenodo ID in manifest by @FriederikeHanssen in #1232
• FIX: Remove check annotation folders existence when no annotation by @maxulysse in #1236
• FIX: Disable JVM hotspot in gatk4 modules by @maxulysse in #1240
• UPDATE: Controlfreec version to 11.6b by @FriederikeHanssen in #1241
• FEAT: Improve schema usage for input by @maxulysse in #1243
• Simplify sentieon test license server usage by @maxulysse in #1242

Full Changelog: 3.3.0...3.3.1