What’s Changed

Added

• Tool: Lofreq callparallel by @AitorPeseta and @nevinwu in https://github.com/nf-core/sarek/pull/1620, https://github.com/nf-core/sarek/pull/1653, https://github.com/nf-core/sarek/pull/1752
• Tool: Indexcov by @lindenb in https://github.com/nf-core/sarek/pull/1613, https://github.com/nf-core/sarek/pull/1752
• Expose fastp parameter --length_required by @LouisLeNezet in https://github.com/nf-core/sarek/pull/1660
• Variant Calling tutorial pages to Usage section by @lescai in https://github.com/nf-core/sarek/pull/1706
• Pipeline level tests by @maxulysse in https://github.com/nf-core/sarek/pull/1661,https://github.com/nf-core/sarek/pull/1669
• Check if flowcell id matches for paired samples by @pmoris in https://github.com/nf-core/sarek/pull/1664
• Documentation on how to use WES ASCAT with chr prefixed bed file by @alexanderchang1 in https://github.com/nf-core/sarek/pull/1638

Changed

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

Fixed

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

Removed

• Retire snpeff_genome by @asp8200 in https://github.com/nf-core/sarek/pull/1656
• Remove Strelka tumor-only somatic variant calling by @nevinwu in https://github.com/nf-core/sarek/pull/1709
• Remove defaults channel from nf-core conda environments by @maxulysse in https://github.com/nf-core/sarek/pull/1663
• Remove defaults channel from local modules by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1755

New Contributors

• @AitorPeseta made their first contribution in https://github.com/nf-core/sarek/pull/1620
• @LouisLeNezet made their first contribution in https://github.com/nf-core/sarek/pull/1660
• @nevinwu made their first contribution in https://github.com/nf-core/sarek/pull/1653
• @pharmlovex made their first contribution in https://github.com/nf-core/sarek/pull/1712
• @pmoris made their first contribution in https://github.com/nf-core/sarek/pull/1664
• @bounlu made their first contribution in https://github.com/nf-core/sarek/pull/1624
• @alexanderchang1 made their first contribution in https://github.com/nf-core/sarek/pull/1638
• @lindenb made their first contribution in https://github.com/nf-core/sarek/pull/1613

Full Changelog: https://github.com/nf-core/sarek/compare/3.4.4…3.5.0

What’s Changed

• FIX: misleading docs - xref 1621 by @maxulysse in https://github.com/nf-core/sarek/pull/1623
• Correct tower snpeff by @cmatKhan in https://github.com/nf-core/sarek/pull/1627
• Allow dbsnp if null in germline variant calling by @cmatKhan in https://github.com/nf-core/sarek/pull/1628

New Contributors

• @cmatKhan made their first contribution in https://github.com/nf-core/sarek/pull/1627

Full Changelog: https://github.com/nf-core/sarek/compare/3.4.3…3.4.4

What’s Changed

Added

• Add support for fastq.gz.spring-files as input by @asp8200 in https://github.com/nf-core/sarek/pull/1534, https://github.com/nf-core/sarek/pull/1573
• Add a specific cnvkit/call module to perform calling from cns files by @lescai in https://github.com/nf-core/sarek/pull/1502
• Adds the cnvkit/export module, to export called CNVs into VCF by @lescai in https://github.com/nf-core/sarek/pull/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 https://github.com/nf-core/sarek/pull/1502
• Simplify logic in args management by @maxulysse in https://github.com/nf-core/sarek/pull/1521
• Update vep cache version to 111 by @maxulysse in https://github.com/nf-core/sarek/pull/1557
• Cleanup + update modules by @maxulysse in https://github.com/nf-core/sarek/pull/1545
• Updating documentation by @asp8200 in https://github.com/nf-core/sarek/pull/1556 and by @maxulysse in https://github.com/nf-core/sarek/pull/1570

Fixed

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

New Contributors

• @famosab made their first contribution in https://github.com/nf-core/sarek/pull/1527
• @YeHW made their first contribution in https://github.com/nf-core/sarek/pull/1563

Full Changelog: https://github.com/nf-core/sarek/compare/3.4.2…3.4.3

What’s Changed

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

New Contributors

• @kenibrewer made their first contribution in https://github.com/nf-core/sarek/pull/1501
• @nh13 made their first contribution in https://github.com/nf-core/sarek/pull/1505

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

New Contributors

• @sminot made their first contribution in https://github.com/nf-core/sarek/pull/1345
• @mirpedrol made their first contribution in https://github.com/nf-core/sarek/pull/1365
• @tdanhorn made their first contribution in https://github.com/nf-core/sarek/pull/1383
• @allaway made their first contribution in https://github.com/nf-core/sarek/pull/1395
• @MatthiasZepper made their first contribution in https://github.com/nf-core/sarek/pull/1420
• @nschcolnicov made their first contribution in https://github.com/nf-core/sarek/pull/1400

Full Changelog: https://github.com/nf-core/sarek/compare/3.4.0…3.4.1

What’s Changed

New tools:

• Dnascope was added by @asp8200 in https://github.com/nf-core/sarek/pull/1193, https://github.com/nf-core/sarek/pull/1280
• Add NGSCheckMate by @SPPearce in https://github.com/nf-core/sarek/pull/1252
• Add CnvkKt Genemetrics by @grantn5 in https://github.com/nf-core/sarek/pull/1223
• Add Bcftools annotate by @grantn5 in https://github.com/nf-core/sarek/pull/1267

Refactoring

• Add an nf-test CI by @adamrtalbot in https://github.com/nf-core/sarek/pull/1288, https://github.com/nf-core/sarek/pull/1289, https://github.com/nf-core/sarek/pull/1290
• Created subworkflow for parsing samplesheet with nf-test by @RaqManzano in https://github.com/nf-core/sarek/pull/1286
• Update config files and other minor code polishing by @maxulysse in https://github.com/nf-core/sarek/pull/1325

Bug fixes and other updates

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

New Contributors

• @grantn5 made their first contribution in https://github.com/nf-core/sarek/pull/1223
• @RaqManzano made their first contribution in https://github.com/nf-core/sarek/pull/1286
• @SPPearce made their first contribution in https://github.com/nf-core/sarek/pull/1252

Full Changelog: https://github.com/nf-core/sarek/compare/3.3.2…3.4.0

What’s Changed

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

Full Changelog: https://github.com/nf-core/sarek/compare/3.3.1…3.3.2

What’s Changed

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

Full Changelog: https://github.com/nf-core/sarek/compare/3.3.0…3.3.1

What’s Changed

• FEAT: Mutect2 multi sample subworkflow by @berguner in https://github.com/nf-core/sarek/pull/1013
• FEAT: Sentieon DNAseq workflow by @asp8200 in https://github.com/nf-core/sarek/pull/994. https://github.com/nf-core/sarek/pull/1002. https://github.com/nf-core/sarek/pull/1007. https://github.com/nf-core/sarek/pull/1123. https://github.com/nf-core/sarek/pull/1044.
• FEAT: Greatly improve tower.yml file by @maxulysse in https://github.com/nf-core/sarek/pull/1197
• FEAT: Use annotation-cache and update VEP to v110 by @maxulysse in https://github.com/nf-core/sarek/pull/1122
• FEAT: Added nf-validation for samplesheet validation by @mirpedrol in https://github.com/nf-core/sarek/pull/1059
• Update of nf-core modules. https://github.com/nf-core/sarek/pull/1180. https://github.com/nf-core/sarek/pull/1160. https://github.com/nf-core/sarek/pull/1174. https://github.com/nf-core/sarek/pull/1227. https://github.com/nf-core/sarek/pull/1224
• Improved docs. https://github.com/nf-core/sarek/pull/1163. https://github.com/nf-core/sarek/pull/1138 (@rhagenson), https://github.com/nf-core/sarek/pull/1192 (@JohannesKersting). https://github.com/nf-core/sarek/pull/1222 (@adamrtalbot). https://github.com/nf-core/sarek/pull/1166. https://github.com/nf-core/sarek/pull/1179 (@robsyme). https://github.com/nf-core/sarek/pull/1183.
• snpeff_db parameter validation by @maxulysse in https://github.com/nf-core/sarek/pull/1143
• FIX: Exome flag for Manta by @maxulysse in https://github.com/nf-core/sarek/pull/1149
• FIX: Move all vep args from ext.args to params.vep_custom_args by @maxulysse in https://github.com/nf-core/sarek/pull/1157
• FIX: GenomicsDB bug with mismatched intervals, remove duplicated variants from VQSR vcfs, add VQSR CI test by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1173
• FIX: Improved workflows for GHA by @adamrtalbot in https://github.com/nf-core/sarek/pull/1200
• FIX: Remove Nextflow caching for CI-tests by @Emiller88 in https://github.com/nf-core/sarek/pull/1202
• FIX: Remove singularity tests from GHA by @maxulysse in https://github.com/nf-core/sarek/pull/1218
• FIX: Better coverage for all tests by @maxulysse in https://github.com/nf-core/sarek/pull/1225, https://github.com/nf-core/sarek/pull/1216
• FIX: GVCF-files are published also when all intervals are processed at once by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1172
• FIX: Don’t pass in intervals file to control-freec for WGS by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1214
• FIX: getpileupsummary should not run if no germline resource is provided by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1171

New Contributors

• @nicorap made their first contribution in https://github.com/nf-core/sarek/pull/1111
• @rhagenson made their first contribution in https://github.com/nf-core/sarek/pull/1138
• @berguner made their first contribution in https://github.com/nf-core/sarek/pull/1013
• @mirpedrol made their first contribution in https://github.com/nf-core/sarek/pull/1059
• @ATpoint made their first contribution in https://github.com/nf-core/sarek/pull/1166
• @JohannesKersting made their first contribution in https://github.com/nf-core/sarek/pull/1192

Full Changelog: https://github.com/nf-core/sarek/compare/3.2.3…3.3.0

What’s Changed

• FIX: Remove public_aws_ecr profile by @maxulysse in https://github.com/nf-core/sarek/pull/1118
• FIX: Remove default null in schema by @maxulysse in https://github.com/nf-core/sarek/pull/1119
• CHORES: Prepare 3.2.3 by @asp8200 in https://github.com/nf-core/sarek/pull/1128
• Release candidate 3.2.3 by @asp8200 in https://github.com/nf-core/sarek/pull/1129

Full Changelog: https://github.com/nf-core/sarek/compare/3.2.2…3.2.3

What’s Changed

• FIX: Fix default memory issue with gatk4/createsequencedictionary by @maxulysse in https://github.com/nf-core/sarek/pull/1087
• Fix ascat manual test by @asp8200 in https://github.com/nf-core/sarek/pull/1093
• FIX: Mutect2 subworkflow by @maxulysse in https://github.com/nf-core/sarek/pull/1098
• FIX: Deepvariant duplicate index by @maxulysse in https://github.com/nf-core/sarek/pull/1100
• FIX: Remove params.tracedir by @maxulysse in https://github.com/nf-core/sarek/pull/1105
• FEAT: Add slack notification for megatests by @maxulysse in https://github.com/nf-core/sarek/pull/1106
• Remove redundant index computation for MD & version for MD Spark by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1101
• update config by @maxulysse in https://github.com/nf-core/sarek/pull/1107
• fix bcftools mpileup by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1109

Full Changelog: https://github.com/nf-core/sarek/compare/3.2.1…3.2.2

What’s Changed

• CHORES: back to dev by @maxulysse in https://github.com/nf-core/sarek/pull/1073
• fix typo in profile name by @maxulysse in https://github.com/nf-core/sarek/pull/1079
• FIX: update bgziptabix module by @maxulysse in https://github.com/nf-core/sarek/pull/1078
• CHORES: Prepare release 3.2.1 by @maxulysse in https://github.com/nf-core/sarek/pull/1080
• FIX: patch more modules by @maxulysse in https://github.com/nf-core/sarek/pull/1082
• Release candidate 3.2.1 by @maxulysse in https://github.com/nf-core/sarek/pull/1081

Full Changelog: https://github.com/nf-core/sarek/compare/3.2.0…3.2.1

What’s Changed

• Back to dev by @maxulysse in https://github.com/nf-core/sarek/pull/859
• replace local subworkflow with nf-core version - vcf_annotate_snpeff by @maxulysse in https://github.com/nf-core/sarek/pull/860
• switch mpileup to bcftools and subset to non-ref by @nickhsmith in https://github.com/nf-core/sarek/pull/832
• add realigned bam export possibilities to gatk4_haplotypecaller by @maxulysse in https://github.com/nf-core/sarek/pull/864
• fix bam output for haplotypecaller by @maxulysse in https://github.com/nf-core/sarek/pull/870
• replace local subworkflow with nf-core version - vcf_annotate_ensemblvep by @maxulysse in https://github.com/nf-core/sarek/pull/865
• nf-core modules update -a by @maxulysse in https://github.com/nf-core/sarek/pull/874
• Concatenating germline vcfs by @asp8200 in https://github.com/nf-core/sarek/pull/792
• Merging template updates 2.7.1 by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/890
• Important! Template update for nf-core/tools v2.7.1 by @nf-core-bot in https://github.com/nf-core/sarek/pull/886
• default results should be null (fails on s3) by @maxulysse in https://github.com/nf-core/sarek/pull/884
• Add skip_tools haplotypecaller_filter by @maxulysse in https://github.com/nf-core/sarek/pull/889
• Remote test warning from nf-core lint by @maxulysse in https://github.com/nf-core/sarek/pull/894
• Fix logic of when to execute tabix on dbsnp by @maxulysse in https://github.com/nf-core/sarek/pull/893
• merge TEMPLATE by @maxulysse in https://github.com/nf-core/sarek/pull/898
• Cache test data on GHA by @maxulysse in https://github.com/nf-core/sarek/pull/909
• Refactor codebase - Part I by @maxulysse in https://github.com/nf-core/sarek/pull/896
• Fix tumor only for freebayes by @maxulysse in https://github.com/nf-core/sarek/pull/927
• Fix pair variant calling issue with msisensor by @maxulysse in https://github.com/nf-core/sarek/pull/929
• Add build_only_index flag by @maxulysse in https://github.com/nf-core/sarek/pull/935
• Add option to download cache for annotation by @maxulysse in https://github.com/nf-core/sarek/pull/936
• FIX: Json validation for lists of tools by @maxulysse in https://github.com/nf-core/sarek/pull/941
• FEAT: Update README by @maxulysse in https://github.com/nf-core/sarek/pull/942
• Add Adam Talbot to contributor list by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/945
• Fix missing annotation keys for vep/snpeff by @maxulysse in https://github.com/nf-core/sarek/pull/954
• Add failsafe options for Nextflow join operator by @maxulysse in https://github.com/nf-core/sarek/pull/957
• update paths by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/965
• ADD: Annotation cache usage docs by @maxulysse in https://github.com/nf-core/sarek/pull/967
• Don’t mutate channel elements in-place by @robsyme in https://github.com/nf-core/sarek/pull/971
• Issue 950: samplesheet validation - no spaces in sample or patient names by @matrulda in https://github.com/nf-core/sarek/pull/978
• ASCAT exome/targeted sequencing resource file generation by @ameynert in https://github.com/nf-core/sarek/pull/981
• Remove exit statements by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/982
• ADD: Cache correctly identifies when it needs to be updated by @maxulysse in https://github.com/nf-core/sarek/pull/985
• Updated ascat for reproducibility by @SusiJo in https://github.com/nf-core/sarek/pull/988
• Issue 952 by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/998
• No need for BAI when using uBAM by @maxulysse in https://github.com/nf-core/sarek/pull/928
• CHORE: update all modules by @maxulysse in https://github.com/nf-core/sarek/pull/968
• CHORES: update subworkflows by @maxulysse in https://github.com/nf-core/sarek/pull/1009
• CHORES: update TEMPLATE with 2.8 by @maxulysse in https://github.com/nf-core/sarek/pull/1011
• Important! Template update for nf-core/tools v2.8 by @nf-core-bot in https://github.com/nf-core/sarek/pull/1010
• fix genome null with annotation by @maxulysse in https://github.com/nf-core/sarek/pull/1014
• Reduce interval groups default for smaller storage consumption by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1015
• Set a default registry outside of profile scope by @maxulysse in https://github.com/nf-core/sarek/pull/1019
• Fix input channels for variantrecalibrator by @asp8200 in https://github.com/nf-core/sarek/pull/1022
• Update pipeline overview by @adamrtalbot in https://github.com/nf-core/sarek/pull/1031
• refactoring by @maxulysse in https://github.com/nf-core/sarek/pull/1012
• update all modules for correct registry usage by @maxulysse in https://github.com/nf-core/sarek/pull/1032
• Remove concatenate_vcfs tests with singularity by @maxulysse in https://github.com/nf-core/sarek/pull/1039
• FIX: dict channel issue when using params.dict by @maxulysse in https://github.com/nf-core/sarek/pull/1040
• ADD: new vep_custom_args by @maxulysse in https://github.com/nf-core/sarek/pull/1041
• FIX: typos by @maxulysse in https://github.com/nf-core/sarek/pull/1043
• Adds public_aws_ecr profile for using ECR hosted images. by @adamrtalbot in https://github.com/nf-core/sarek/pull/1045
• Input validation fixes by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1048
• CHORES: modules update by @maxulysse in https://github.com/nf-core/sarek/pull/1051
• Disable GATK filters when joint calling by @amizeranschi in https://github.com/nf-core/sarek/pull/1050
• FIX: VCFTOOLS public ecr registry by @maxulysse in https://github.com/nf-core/sarek/pull/1058
• CHORES: bump to 3.2.0 by @maxulysse in https://github.com/nf-core/sarek/pull/1056
• remove exit strategy for MANTA/STRELKA by @maxulysse in https://github.com/nf-core/sarek/pull/882
• FIX: pattern for fasta file by @maxulysse in https://github.com/nf-core/sarek/pull/1055
• FIX: automatic restart from step by @maxulysse in https://github.com/nf-core/sarek/pull/1062
• FIX: join duplication for manta/strelka annotation by @maxulysse in https://github.com/nf-core/sarek/pull/1063
• don’t publish genomicsdb files by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1061
• CHORES: remove version from pictures by @maxulysse in https://github.com/nf-core/sarek/pull/1070
• docs update by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1071
• Candidate release 3.2.0 by @maxulysse in https://github.com/nf-core/sarek/pull/1057

New Contributors

• @robsyme made their first contribution in https://github.com/nf-core/sarek/pull/971
• @matrulda made their first contribution in https://github.com/nf-core/sarek/pull/978
• @ameynert made their first contribution in https://github.com/nf-core/sarek/pull/981
• @adamrtalbot made their first contribution in https://github.com/nf-core/sarek/pull/1031
• @amizeranschi made their first contribution in https://github.com/nf-core/sarek/pull/1050

Full Changelog: https://github.com/nf-core/sarek/compare/3.1.2…3.2.0

What’s Changed

• Release 3.1.2 by @maxulysse in https://github.com/nf-core/sarek/pull/906

Full Changelog: https://github.com/nf-core/sarek/compare/3.1.1…3.1.2

What’s Changed

• Syn up dev by @maxulysse in https://github.com/nf-core/sarek/pull/849
• Remove “None” definition from schema by @drpatelh in https://github.com/nf-core/sarek/pull/851
• Md cram update by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/855
• Add R64-1-1 and UMD3.1 by @maxulysse in https://github.com/nf-core/sarek/pull/856
• prepare release 3.1.1 by @maxulysse in https://github.com/nf-core/sarek/pull/858
• release 3.1.1 by @maxulysse in https://github.com/nf-core/sarek/pull/857

Full Changelog: https://github.com/nf-core/sarek/compare/3.1…3.1.1

What’s Changed

• Back to business on dev by @maxulysse in https://github.com/nf-core/sarek/pull/762
• Update subway map by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/766
• Dev deepvariant by @maxulysse in https://github.com/nf-core/sarek/pull/768
• Fix gatk4 cnnscorevariants by @maxulysse in https://github.com/nf-core/sarek/pull/770
• add logo for Danish National Genome Center by @maxulysse in https://github.com/nf-core/sarek/pull/774
• update to new modules syntax + patch on non-up to date modules by @maxulysse in https://github.com/nf-core/sarek/pull/771
• nf core template merge 2.6 by @maxulysse in https://github.com/nf-core/sarek/pull/773
• AWS outdir paths were mixed up by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/777
• Add this years posters by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/775
• use chr length file by default since cf is otherwise not working by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/783
• No scatter on full size tests to avoid issues with in or output files randomly not staged by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/782
• Updated docs of bcftools stats variant depth by @SusiJo in https://github.com/nf-core/sarek/pull/788
• ci: Move tmpdir to ~ by @Emiller88 in https://github.com/nf-core/sarek/pull/791
• Fix somatic test with mutect2 by @SusiJo in https://github.com/nf-core/sarek/pull/790
• Md cram by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/735
• don’t annotate gvcfs by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/793
• Don’t publish unzip files by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/794
• Update ci.yml by @maxulysse in https://github.com/nf-core/sarek/pull/796
• Update all subworkflows name by @maxulysse in https://github.com/nf-core/sarek/pull/784
• Fix sample header error when starting from bams by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/807
• More complete CI by @maxulysse in https://github.com/nf-core/sarek/pull/806
• add rgid, to separate sample info by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/814
• Fix validation of input when launching from website by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/813
• collect cnvkit reference to not be consumed by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/817
• prioritze test conf for mutect in tests by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/815
• Use putIfAbsent by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/821
• add speed up parameters for genomicsdb by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/827
• Add option for cnvkit to provide external Cnn reference by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/825
• add more docs about scatter/gather by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/820
• Fix bug with no variantcalling when starting from step recalibration Issue 763 by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/828
• Update modules & tool versions by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/822
• Get ride of copyTo to enable s3 buckets in different regiosn by @maxulysse in https://github.com/nf-core/sarek/pull/839
• remove cf len file from config by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/841
• increase samtools stats memory by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/842

Full Changelog: https://github.com/nf-core/sarek/compare/3.0.2…3.1

What’s Changed

• Fix Vep plugin usage by @BarryDigby in https://github.com/nf-core/sarek/pull/688
• Fix when clause for building mapping indexes by @maxulysse in https://github.com/nf-core/sarek/pull/689
• Updating nf-core-modules by @asp8200 in https://github.com/nf-core/sarek/pull/685, https://github.com/nf-core/sarek/pull/734
• Fix schema for controlfreec ploidy by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/704
• Vep Issues: loftee needs version by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/706
• Adding md5-sums to the test-yml-files by @asp8200 in https://github.com/nf-core/sarek/pull/696
• sync 2.5 by @maxulysse in https://github.com/nf-core/sarek/pull/720
• Dev sync 2.5.1 by @maxulysse in https://github.com/nf-core/sarek/pull/723
• Subway update by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/719
• Add in Azure config documentation by @vsmalladi in https://github.com/nf-core/sarek/pull/716
• Add further support ControlFreec for targeted data by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/728
• Allow interval.{bed,interval,interval_list} files by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/727
• Switch germline and somatic full tests by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/731
• Optimize resource requests by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/726
• Add testing for conda/singularity by @maxulysse in https://github.com/nf-core/sarek/pull/736, https://github.com/nf-core/sarek/pull/691
• Clean up publishing by @FriederikeHanssen and @maxulysse in https://github.com/nf-core/sarek/pull/741, https://github.com/nf-core/sarek/pull/705, https://github.com/nf-core/sarek/pull/681
• Additional input checks by @asp8200 in https://github.com/nf-core/sarek/pull/742
• Test profiles separated into multiple files to support usage with tower by @maxulysse in https://github.com/nf-core/sarek/pull/743, https://github.com/nf-core/sarek/pull/692
• Remove errorStrategy in modules.config by @drpatelh in https://github.com/nf-core/sarek/pull/757
• update zenodo link to point to latest by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/758

New Contributors

• @BarryDigby made their first contribution in https://github.com/nf-core/sarek/pull/688
• @vsmalladi made their first contribution in https://github.com/nf-core/sarek/pull/715
• @drpatelh made their first contribution in https://github.com/nf-core/sarek/pull/757

Full Changelog: https://github.com/nf-core/sarek/compare/3.0.1…3.0.2

What’s Changed

• Fix usage of intervals in samtools/mpileup by @nickhsmith in https://github.com/nf-core/sarek/pull/708

Full Changelog: https://github.com/nf-core/sarek/compare/3.0…3.0.1

• Porting to DSL2
• Use CRAM files where possible
• Add new tools: DragMap, DeepVariant, Joint germline calling, Haplotypecaller single sample, CNVKit Somatic, Tiddit Somatic
• Replaced tools: Trimgalore -> Fastp, Qualimap -> Mosdepth
• New references: BWAMem2, DragMap, Germline Resource
• Add a new entry --step markduplicates
• Steps can be started from bam or cram files
• Added --paired_variant_calling_only to skip normal computations for paired samples
• Only unmatched tumor samples will be run in single mode
• Input fastq files are split by default and mapped in parallel
• Bam2Fastq: changed to using samtools
• Samplesheet is now in CSV format with a header line with improved validation and flexibility
• New parameter --skip_tools retires --skip_qc, --skip_markduplicates and --skip_bqsr
• --sequencing_center renamed to —seq_platform`
• New parameter --wes must be set for targeted data
• New parameter --save_bam_ouput to store results file in BAM format instead of CRAM
• Additional VEP output formats
• Additional VEP plugins: loftee, spliceAI, spliceRegions, dbnsfp
• Remove sentieon support

New Contributors

• @abhi18av made their first contribution in https://github.com/nf-core/sarek/pull/394
• @nickhsmith made their first contribution in https://github.com/nf-core/sarek/pull/454
• @Emiller88 made their first contribution in https://github.com/nf-core/sarek/pull/465
• @priesgo made their first contribution in https://github.com/nf-core/sarek/pull/432
• @SusiJo made their first contribution in https://github.com/nf-core/sarek/pull/545
• @asp8200 made their first contribution in https://github.com/nf-core/sarek/pull/571
• @lassefolkersen made their first contribution in https://github.com/nf-core/sarek/pull/591
• @WackerO made their first contribution in https://github.com/nf-core/sarek/pull/570

Full Changelog: https://github.com/nf-core/sarek/compare/2.7.2…3.0

What’s Changed

• Fix MapReads caching bug by @BrunoGrandePhD in https://github.com/nf-core/sarek/pull/566

Full Changelog: https://github.com/nf-core/sarek/compare/2.7.1…2.7.2

• Add tumor only mode for Mutect2 and MSIsensor
• Add --cf_contamination_adjustment params to adjust contamination with Control-FREEC (356)
• Add --cf_contamination params to specify contamination value with Control-FREEC (372)
• Sync TEMPLATE with tools 1.14 (#373)
• Fix Spark related issue due to Docker settings in nextflow.config

See full CHANGELOG, for more information

• Add UMI annotation and consensus functionality to Sarek (#145)
• Add ignore_soft_clipped_bases option for GATK Mutect2 (#230)
• Add --aligner to choose between bwa and bwa-mem2 (#237, #282)
• Add WES and tumor-only mode for Control-FREEC (#302, #304)
• Update Control-FREEC from 11.5 to 11.6
• --no_gatk_spark is now removed, use --use_gatk_spark if you want to use GATK Spark
• --no_gvcf is now removed, use --generate_gvcf if you want *.g.vcf files from GATK HaplotypeCaller

See full CHANGELOG, for more information

• Update GATK from 4.1.6.0 to 4.1.7.0 (#214)
• Fix channels collision between Freebayes and Mutect2 (#214)
• Fix Mutect2 issue #210 (#214)
• Add awsfulltest.yml GitHub Actions workflow (#219)

See full CHANGELOG, for more information

• Add GATK Spark possibilities (#76)
• Add CNVkit (#153)
• Add MSIsensor (#163)
• Improve support for minimal genome (only fasta)
• Output directory DuplicateMarked is now replaced by DuplicatesMarked
• Output directory controlFREEC is now replaced by Control-FREEC
• Fix annotation CI testing with snpEff and VEP (#143)
• Fix --no_intervals for Mutect2 (#146)
• Add --skip_markduplicates (#205)

See full CHANGELOG, for more information

• Add mouse (GRCm38) support (#52)
• Add minimal support for minimal genome (only fasta or fasta + knownIndels) (#60)
• Add new params split_fastq (#61)
• Fix issue with .interval_list file from the GATK bundle (#58)
• Fix issue with label memory_max for BaseRecalibrator process (#73)

See full CHANGELOG, for more information

• Fix singularity.autoMounts issue (#48)
• Use correct tag for annotation containers (#49)
• Fix paths for scripts (#50)

See full CHANGELOG, for more information

• First release within nf-core
• Compliant within all nf-core requirements
  • One script to rule them all
  • Full AWS iGenomes support
• Adds PON for Mutect2
• Adds TIDDIT for Germline sample
• Adds Control-FREEC for CNV
• Change in parameter names:
  • sampleDir, sample and annotateVCF are now input
  • genomeFile is now fasta
  • genomeIndex is now fastaFai
  • genomeDict is now dict

See full CHANGELOG, for more information