nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
annotationcancergatk4genomicsgermlinepre-processingsomatictarget-panelsvariant-callingwhole-exome-sequencingwhole-genome-sequencing
Version history
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_intervalsusage and CPU allocation in #1928 by @SPPearce - DeepVariant configuration: Added
--sample_nameargument 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 https://github.com/nf-core/sarek/pull/1767 by @FriederikeHanssen
- Merge intervals for WES in GATK GenomicsDBImport in https://github.com/nf-core/sarek/pull/1777 by @tdanhorn
Fixed
- Use file-path-pattern over file-path to hanlde glob for known_indels and known_indels_tbi to fix https://github.com/nf-core/sarek/issues/1785 in https://github.com/nf-core/sarek/pull/1797 by @maxulysse
- Update GHA for full_test tests in https://github.com/nf-core/sarek/pull/1802 by @maxulysse
Full Changelog: https://github.com/nf-core/sarek/compare/3.5.0…3.5.1
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_requiredby @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
chrprefixedbedfile 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
defaultschannel from nf-core conda environments by @maxulysse in https://github.com/nf-core/sarek/pull/1663 - Remove
defaultschannel 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-validationfor 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_dbparameter 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_onlyto 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_toolsretires--skip_qc,--skip_markduplicatesand--skip_bqsr --sequencing_centerrenamed to —seq_platform`- New parameter
--wesmust be set for targeted data - New parameter
--save_bam_ouputto 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
MapReadscaching 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
Mutect2andMSIsensor - Add
--cf_contamination_adjustmentparams to adjust contamination withControl-FREEC(356) - Add
--cf_contaminationparams to specify contamination value withControl-FREEC(372) - Sync TEMPLATE with tools 1.14 (#373)
- Fix
Sparkrelated issue due toDockersettings innextflow.config
See full CHANGELOG, for more information
- Add
UMIannotation and consensus functionality to Sarek (#145) - Add
ignore_soft_clipped_basesoption forGATK Mutect2(#230) - Add
--alignerto choose betweenbwaandbwa-mem2(#237, #282) - Add WES and tumor-only mode for Control-FREEC (#302, #304)
- Update
Control-FREECfrom11.5to11.6 --no_gatk_sparkis now removed, use--use_gatk_sparkif you want to useGATK Spark--no_gvcfis now removed, use--generate_gvcfif you want*.g.vcffiles fromGATK HaplotypeCaller
See full CHANGELOG, for more information
- Update GATK from
4.1.6.0to4.1.7.0(#214) - Fix channels collision between
FreebayesandMutect2(#214) - Fix
Mutect2issue #210 (#214) - Add
awsfulltest.ymlGitHub Actions workflow (#219)
See full CHANGELOG, for more information
- Add
GATK Sparkpossibilities (#76) - Add
CNVkit(#153) - Add
MSIsensor(#163) - Improve support for minimal genome (only fasta)
- Output directory
DuplicateMarkedis now replaced byDuplicatesMarked - Output directory
controlFREECis now replaced byControl-FREEC - Fix annotation CI testing with
snpEffandVEP(#143) - Fix
--no_intervalsforMutect2(#146) - Add
--skip_markduplicates(#205)
See full CHANGELOG, for more information
- Add mouse (GRCm38) support (#52)
- Add minimal support for minimal genome (only
fastaorfasta+knownIndels) (#60) - Add new params
split_fastq(#61) - Fix issue with
.interval_listfile from theGATKbundle (#58) - Fix issue with label
memory_maxforBaseRecalibratorprocess (#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-corerequirements- One script to rule them all
- Full AWS iGenomes support
- Adds PON for
Mutect2 - Adds
TIDDITfor Germline sample - Adds
Control-FREECfor CNV - Change in parameter names:
sampleDir,sampleandannotateVCFare nowinputgenomeFileis nowfastagenomeIndexis nowfastaFaigenomeDictis nowdict
See full CHANGELOG, for more information
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